From 6606df2233b63f28907340b0625e6bb5d7ecd1f2 Mon Sep 17 00:00:00 2001 From: Simon Duerr Date: Wed, 11 Nov 2020 13:27:21 +0100 Subject: [PATCH] ob3.1 compatibility update, added Dockerfile for running automated unit tests --- .github/workflows/main.yml | 18 + Dockerfile | 55 + environment.yml | 27 + evaluators.py | 2 +- main.py | 2 +- src/JobConfig.py | 2 +- src/MoleculeCreator.py | 84 +- src/MoleculeInfo.py | 19 +- src/gaapi/Individual.py | 2 +- src/gaapi/generators.py | 2 +- src/outprocesses.py | 2 +- unittests/example_files/H1A19.pdb | 112 +- unittests/example_files/H1A19_ob2.4.2.pdb | 442 + .../example_files/H1A19_ob2.4.2_resname.pdb | 442 + unittests/example_files/H1A19_resname.pdb | 112 +- unittests/example_files/openmm_entropy.in | 55 + .../output_files/applied_composition.pdb | 84 +- unittests/output_files/leap.log | 372732 +++++++++++++++ unittests/output_files/mol.pdb | 428 +- unittests/output_files/mol.prmtop | 12 +- unittests/output_files/test_gly_to_K.pdb | 410 +- .../test_thr_to_gly_restypeFalse.pdb | 402 +- .../test_thr_to_gly_restypeTrue.pdb | 402 +- .../test_thr_to_his_restypeFalse.pdb | 428 +- .../test_thr_to_his_restypeTrue.pdb | 428 +- unittests/run_unitests.sh | 4 +- unittests/test_StartGA_Run.py | 10 +- unittests/test_openbabel.py | 2 +- 28 files changed, 375264 insertions(+), 1456 deletions(-) create mode 100644 .github/workflows/main.yml create mode 100644 Dockerfile create mode 100644 environment.yml create mode 100644 unittests/example_files/H1A19_ob2.4.2.pdb create mode 100644 unittests/example_files/H1A19_ob2.4.2_resname.pdb create mode 100644 unittests/example_files/openmm_entropy.in 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/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/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 bb92c46..b2ba470 100755 --- a/evaluators.py +++ b/evaluators.py @@ -15,7 +15,7 @@ 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 diff --git a/main.py b/main.py index fd93b12..4bb1282 100755 --- a/main.py +++ b/main.py @@ -15,7 +15,7 @@ from past.utils import old_div import numpy as np import argparse -import openbabel +from openbabel import openbabel import time import json import sys diff --git a/src/JobConfig.py b/src/JobConfig.py index 59080d5..e31490a 100755 --- a/src/JobConfig.py +++ b/src/JobConfig.py @@ -19,7 +19,7 @@ from src.gaapi import operator_types import sys import os -import openbabel +from openbabel import openbabel import collections from src import constants as cnts diff --git a/src/MoleculeCreator.py b/src/MoleculeCreator.py index 943d452..c53f304 100755 --- a/src/MoleculeCreator.py +++ b/src/MoleculeCreator.py @@ -11,17 +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 -# 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 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 @@ -116,17 +118,19 @@ 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() @@ -135,7 +139,7 @@ def add_fragment(mol, fragment, id_start): 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): @@ -168,12 +172,11 @@ def swapsidechain(settings, mol, res_index, aa_mol): """ mol.BeginModify() - + aa_mol.BeginModify() curr = mol.GetResidue(res_index) new = aa_mol.GetResidue(0) - print(mol, mol.NumResidues()) - print(mol.GetResidue(4)) + mol_CA = mi.getAlphaCarbon(curr) mol_CB = mi.getBetaAtom(curr) mol_N = mi.getBBNitrogen(curr) @@ -183,11 +186,12 @@ def swapsidechain(settings, mol, res_index, aa_mol): aa_bb_nitrogen = mi.getBBNitrogen(new) aa_gamma_atom = mi.getChi1DihedralAtom(new) - frag_res = aa_CB.GetResidue() + frag_res = new frag_name = frag_res.GetName() - res_name =mi.getResType(curr) + res_name =mi.getResType(curr) + aa_tor = 0 if (aa_gamma_atom is not None): aa_tor = aa_mol.GetTorsion(aa_gamma_atom, aa_CA, aa_CB, aa_bb_nitrogen) @@ -232,6 +236,7 @@ def swapsidechain(settings, 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)): @@ -243,7 +248,7 @@ def swapsidechain(settings, 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]) @@ -258,8 +263,8 @@ def swapsidechain(settings, 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()) @@ -282,21 +287,30 @@ def swapsidechain(settings, 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) - + 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)) + + # 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) + + 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 @@ -335,24 +349,34 @@ def swapsidechain(settings, mol, res_index, aa_mol): for obatom in openbabel.OBResidueAtomIter(curr): if curr.GetAtomID(obatom) in ["HE3", "HE4", "HE5", "HE6", "HE7", "HE8"]: curr.SetAtomID(obatom, "HE1") - + + # 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.WriteFile(mol, "temp.pdb") + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("pdb", "pdb") + obConversion.ReadFile(mol, "temp.pdb") + os.remove('temp.pdb') + + # 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) - + + ## Here the correct dihedral needs to be set! 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) + diff --git a/src/MoleculeInfo.py b/src/MoleculeInfo.py index 5aac834..3d095b6 100755 --- a/src/MoleculeInfo.py +++ b/src/MoleculeInfo.py @@ -12,12 +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 -# from openbabel import openbabel -# from openbabel.openbabel import OBResidue -# from openbabel.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 @@ -86,7 +86,7 @@ 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): @@ -185,7 +185,7 @@ def getBetaAtom(obres): obres : OBResidue Query residue """ - + alpha_carbon = getAlphaCarbon(obres) bbcarboxyl = getBBCarboxyl(obres) @@ -206,7 +206,7 @@ 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'): @@ -604,6 +604,7 @@ def getChi1DihedralAtom(obres): beta_atom = getBetaAtom(obres) gamma_atom = None + if beta_atom is None: return None diff --git a/src/gaapi/Individual.py b/src/gaapi/Individual.py index 11facd8..35d7a85 100755 --- a/src/gaapi/Individual.py +++ b/src/gaapi/Individual.py @@ -13,7 +13,7 @@ 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 diff --git a/src/gaapi/generators.py b/src/gaapi/generators.py index be61ee8..14bf6d7 100755 --- a/src/gaapi/generators.py +++ b/src/gaapi/generators.py @@ -14,7 +14,7 @@ import numpy as np from src import MoleculeInfo as mi -import openbabel +from openbabel import openbabel def initialisePopulation(settings): diff --git a/src/outprocesses.py b/src/outprocesses.py index 3a63478..cc9427f 100644 --- a/src/outprocesses.py +++ b/src/outprocesses.py @@ -17,7 +17,7 @@ import os import subprocess import numpy as np -import openbabel +from openbabel import openbabel import time diff --git a/unittests/example_files/H1A19.pdb b/unittests/example_files/H1A19.pdb index 17c0c4e..c9a19ba 100644 --- a/unittests/example_files/H1A19.pdb +++ b/unittests/example_files/H1A19.pdb @@ -10,16 +10,16 @@ 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 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 -0.694 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 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 @@ -223,25 +223,25 @@ CONECT 1 2 CONECT 2 1 3 4 5 CONECT 3 2 CONECT 4 2 -CONECT 5 2 6 7 -CONECT 6 5 +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 11 12 13 9 +CONECT 10 9 11 12 13 CONECT 11 10 CONECT 12 10 -CONECT 13 10 14 19 +CONECT 13 10 14 19 19 CONECT 14 13 15 16 CONECT 15 14 -CONECT 16 14 17 18 +CONECT 16 14 17 18 18 CONECT 17 16 -CONECT 18 16 19 -CONECT 19 13 18 20 +CONECT 18 16 16 19 +CONECT 19 13 13 18 20 CONECT 20 19 CONECT 21 9 -CONECT 22 9 23 24 -CONECT 23 22 +CONECT 22 9 23 23 24 +CONECT 23 22 22 CONECT 24 22 25 26 CONECT 25 24 CONECT 26 24 27 28 32 @@ -250,8 +250,8 @@ CONECT 28 26 29 30 31 CONECT 29 28 CONECT 30 28 CONECT 31 28 -CONECT 32 26 33 34 -CONECT 33 32 +CONECT 32 26 33 33 34 +CONECT 33 32 32 CONECT 34 32 35 36 CONECT 35 34 CONECT 36 34 37 38 42 @@ -260,8 +260,8 @@ CONECT 38 36 39 40 41 CONECT 39 38 CONECT 40 38 CONECT 41 38 -CONECT 42 36 43 44 -CONECT 43 42 +CONECT 42 36 43 43 44 +CONECT 43 42 42 CONECT 44 42 45 46 CONECT 45 44 CONECT 46 44 47 48 52 @@ -270,8 +270,8 @@ CONECT 48 46 49 50 51 CONECT 49 48 CONECT 50 48 CONECT 51 48 -CONECT 52 46 53 54 -CONECT 53 52 +CONECT 52 46 53 53 54 +CONECT 53 52 52 CONECT 54 52 55 56 CONECT 55 54 CONECT 56 54 57 58 62 @@ -280,8 +280,8 @@ CONECT 58 56 59 60 61 CONECT 59 58 CONECT 60 58 CONECT 61 58 -CONECT 62 56 63 64 -CONECT 63 62 +CONECT 62 56 63 63 64 +CONECT 63 62 62 CONECT 64 62 65 66 CONECT 65 64 CONECT 66 64 67 68 72 @@ -290,8 +290,8 @@ CONECT 68 66 69 70 71 CONECT 69 68 CONECT 70 68 CONECT 71 68 -CONECT 72 66 73 74 -CONECT 73 72 +CONECT 72 66 73 73 74 +CONECT 73 72 72 CONECT 74 72 75 76 CONECT 75 74 CONECT 76 74 77 78 82 @@ -300,8 +300,8 @@ CONECT 78 76 79 80 81 CONECT 79 78 CONECT 80 78 CONECT 81 78 -CONECT 82 76 83 84 -CONECT 83 82 +CONECT 82 76 83 83 84 +CONECT 83 82 82 CONECT 84 82 85 86 CONECT 85 84 CONECT 86 84 87 88 92 @@ -310,8 +310,8 @@ CONECT 88 86 89 90 91 CONECT 89 88 CONECT 90 88 CONECT 91 88 -CONECT 92 86 93 94 -CONECT 93 92 +CONECT 92 86 93 93 94 +CONECT 93 92 92 CONECT 94 92 95 96 CONECT 95 94 CONECT 96 94 97 98 102 @@ -320,8 +320,8 @@ CONECT 98 96 99 100 101 CONECT 99 98 CONECT 100 98 CONECT 101 98 -CONECT 102 96 103 104 -CONECT 103 102 +CONECT 102 96 103 103 104 +CONECT 103 102 102 CONECT 104 102 105 106 CONECT 105 104 CONECT 106 104 107 108 112 @@ -330,8 +330,8 @@ CONECT 108 106 109 110 111 CONECT 109 108 CONECT 110 108 CONECT 111 108 -CONECT 112 106 113 114 -CONECT 113 112 +CONECT 112 106 113 113 114 +CONECT 113 112 112 CONECT 114 112 115 116 CONECT 115 114 CONECT 116 114 117 118 122 @@ -340,8 +340,8 @@ CONECT 118 116 119 120 121 CONECT 119 118 CONECT 120 118 CONECT 121 118 -CONECT 122 116 123 124 -CONECT 123 122 +CONECT 122 116 123 123 124 +CONECT 123 122 122 CONECT 124 122 125 126 CONECT 125 124 CONECT 126 124 127 128 132 @@ -350,8 +350,8 @@ CONECT 128 126 129 130 131 CONECT 129 128 CONECT 130 128 CONECT 131 128 -CONECT 132 126 133 134 -CONECT 133 132 +CONECT 132 126 133 133 134 +CONECT 133 132 132 CONECT 134 132 135 136 CONECT 135 134 CONECT 136 134 137 138 142 @@ -360,8 +360,8 @@ CONECT 138 136 139 140 141 CONECT 139 138 CONECT 140 138 CONECT 141 138 -CONECT 142 136 143 144 -CONECT 143 142 +CONECT 142 136 143 143 144 +CONECT 143 142 142 CONECT 144 142 145 146 CONECT 145 144 CONECT 146 144 147 148 152 @@ -370,8 +370,8 @@ CONECT 148 146 149 150 151 CONECT 149 148 CONECT 150 148 CONECT 151 148 -CONECT 152 146 153 154 -CONECT 153 152 +CONECT 152 146 153 153 154 +CONECT 153 152 152 CONECT 154 152 155 156 CONECT 155 154 CONECT 156 154 157 158 162 @@ -380,8 +380,8 @@ CONECT 158 156 159 160 161 CONECT 159 158 CONECT 160 158 CONECT 161 158 -CONECT 162 156 163 164 -CONECT 163 162 +CONECT 162 156 163 163 164 +CONECT 163 162 162 CONECT 164 162 165 166 CONECT 165 164 CONECT 166 164 167 168 172 @@ -390,8 +390,8 @@ CONECT 168 166 169 170 171 CONECT 169 168 CONECT 170 168 CONECT 171 168 -CONECT 172 166 173 174 -CONECT 173 172 +CONECT 172 166 173 173 174 +CONECT 173 172 172 CONECT 174 172 175 176 CONECT 175 174 CONECT 176 174 177 178 182 @@ -400,8 +400,8 @@ CONECT 178 176 179 180 181 CONECT 179 178 CONECT 180 178 CONECT 181 178 -CONECT 182 176 183 184 -CONECT 183 182 +CONECT 182 176 183 183 184 +CONECT 183 182 182 CONECT 184 182 185 186 CONECT 185 184 CONECT 186 184 187 188 192 @@ -410,8 +410,8 @@ CONECT 188 186 189 190 191 CONECT 189 188 CONECT 190 188 CONECT 191 188 -CONECT 192 186 193 194 -CONECT 193 192 +CONECT 192 186 193 193 194 +CONECT 193 192 192 CONECT 194 192 195 196 CONECT 195 194 CONECT 196 194 197 198 202 @@ -420,8 +420,8 @@ CONECT 198 196 199 200 201 CONECT 199 198 CONECT 200 198 CONECT 201 198 -CONECT 202 196 203 204 -CONECT 203 202 +CONECT 202 196 203 203 204 +CONECT 203 202 202 CONECT 204 202 205 206 CONECT 205 204 CONECT 206 204 207 208 212 @@ -430,8 +430,8 @@ CONECT 208 206 209 210 211 CONECT 209 208 CONECT 210 208 CONECT 211 208 -CONECT 212 206 213 214 -CONECT 213 212 +CONECT 212 206 213 213 214 +CONECT 213 212 212 CONECT 214 212 215 216 CONECT 215 214 CONECT 216 214 217 218 219 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 index 3375614..7165682 100644 --- a/unittests/example_files/H1A19_resname.pdb +++ b/unittests/example_files/H1A19_resname.pdb @@ -10,16 +10,16 @@ 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 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 -0.694 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 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 @@ -223,25 +223,25 @@ CONECT 1 2 CONECT 2 1 3 4 5 CONECT 3 2 CONECT 4 2 -CONECT 5 2 6 7 -CONECT 6 5 +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 11 12 13 9 +CONECT 10 9 11 12 13 CONECT 11 10 CONECT 12 10 -CONECT 13 10 14 19 +CONECT 13 10 14 19 19 CONECT 14 13 15 16 CONECT 15 14 -CONECT 16 14 17 18 +CONECT 16 14 17 18 18 CONECT 17 16 -CONECT 18 16 19 -CONECT 19 13 18 20 +CONECT 18 16 16 19 +CONECT 19 13 13 18 20 CONECT 20 19 CONECT 21 9 -CONECT 22 9 23 24 -CONECT 23 22 +CONECT 22 9 23 23 24 +CONECT 23 22 22 CONECT 24 22 25 26 CONECT 25 24 CONECT 26 24 27 28 32 @@ -250,8 +250,8 @@ CONECT 28 26 29 30 31 CONECT 29 28 CONECT 30 28 CONECT 31 28 -CONECT 32 26 33 34 -CONECT 33 32 +CONECT 32 26 33 33 34 +CONECT 33 32 32 CONECT 34 32 35 36 CONECT 35 34 CONECT 36 34 37 38 42 @@ -260,8 +260,8 @@ CONECT 38 36 39 40 41 CONECT 39 38 CONECT 40 38 CONECT 41 38 -CONECT 42 36 43 44 -CONECT 43 42 +CONECT 42 36 43 43 44 +CONECT 43 42 42 CONECT 44 42 45 46 CONECT 45 44 CONECT 46 44 47 48 52 @@ -270,8 +270,8 @@ CONECT 48 46 49 50 51 CONECT 49 48 CONECT 50 48 CONECT 51 48 -CONECT 52 46 53 54 -CONECT 53 52 +CONECT 52 46 53 53 54 +CONECT 53 52 52 CONECT 54 52 55 56 CONECT 55 54 CONECT 56 54 57 58 62 @@ -280,8 +280,8 @@ CONECT 58 56 59 60 61 CONECT 59 58 CONECT 60 58 CONECT 61 58 -CONECT 62 56 63 64 -CONECT 63 62 +CONECT 62 56 63 63 64 +CONECT 63 62 62 CONECT 64 62 65 66 CONECT 65 64 CONECT 66 64 67 68 72 @@ -290,8 +290,8 @@ CONECT 68 66 69 70 71 CONECT 69 68 CONECT 70 68 CONECT 71 68 -CONECT 72 66 73 74 -CONECT 73 72 +CONECT 72 66 73 73 74 +CONECT 73 72 72 CONECT 74 72 75 76 CONECT 75 74 CONECT 76 74 77 78 82 @@ -300,8 +300,8 @@ CONECT 78 76 79 80 81 CONECT 79 78 CONECT 80 78 CONECT 81 78 -CONECT 82 76 83 84 -CONECT 83 82 +CONECT 82 76 83 83 84 +CONECT 83 82 82 CONECT 84 82 85 86 CONECT 85 84 CONECT 86 84 87 88 92 @@ -310,8 +310,8 @@ CONECT 88 86 89 90 91 CONECT 89 88 CONECT 90 88 CONECT 91 88 -CONECT 92 86 93 94 -CONECT 93 92 +CONECT 92 86 93 93 94 +CONECT 93 92 92 CONECT 94 92 95 96 CONECT 95 94 CONECT 96 94 97 98 102 @@ -320,8 +320,8 @@ CONECT 98 96 99 100 101 CONECT 99 98 CONECT 100 98 CONECT 101 98 -CONECT 102 96 103 104 -CONECT 103 102 +CONECT 102 96 103 103 104 +CONECT 103 102 102 CONECT 104 102 105 106 CONECT 105 104 CONECT 106 104 107 108 112 @@ -330,8 +330,8 @@ CONECT 108 106 109 110 111 CONECT 109 108 CONECT 110 108 CONECT 111 108 -CONECT 112 106 113 114 -CONECT 113 112 +CONECT 112 106 113 113 114 +CONECT 113 112 112 CONECT 114 112 115 116 CONECT 115 114 CONECT 116 114 117 118 122 @@ -340,8 +340,8 @@ CONECT 118 116 119 120 121 CONECT 119 118 CONECT 120 118 CONECT 121 118 -CONECT 122 116 123 124 -CONECT 123 122 +CONECT 122 116 123 123 124 +CONECT 123 122 122 CONECT 124 122 125 126 CONECT 125 124 CONECT 126 124 127 128 132 @@ -350,8 +350,8 @@ CONECT 128 126 129 130 131 CONECT 129 128 CONECT 130 128 CONECT 131 128 -CONECT 132 126 133 134 -CONECT 133 132 +CONECT 132 126 133 133 134 +CONECT 133 132 132 CONECT 134 132 135 136 CONECT 135 134 CONECT 136 134 137 138 142 @@ -360,8 +360,8 @@ CONECT 138 136 139 140 141 CONECT 139 138 CONECT 140 138 CONECT 141 138 -CONECT 142 136 143 144 -CONECT 143 142 +CONECT 142 136 143 143 144 +CONECT 143 142 142 CONECT 144 142 145 146 CONECT 145 144 CONECT 146 144 147 148 152 @@ -370,8 +370,8 @@ CONECT 148 146 149 150 151 CONECT 149 148 CONECT 150 148 CONECT 151 148 -CONECT 152 146 153 154 -CONECT 153 152 +CONECT 152 146 153 153 154 +CONECT 153 152 152 CONECT 154 152 155 156 CONECT 155 154 CONECT 156 154 157 158 162 @@ -380,8 +380,8 @@ CONECT 158 156 159 160 161 CONECT 159 158 CONECT 160 158 CONECT 161 158 -CONECT 162 156 163 164 -CONECT 163 162 +CONECT 162 156 163 163 164 +CONECT 163 162 162 CONECT 164 162 165 166 CONECT 165 164 CONECT 166 164 167 168 172 @@ -390,8 +390,8 @@ CONECT 168 166 169 170 171 CONECT 169 168 CONECT 170 168 CONECT 171 168 -CONECT 172 166 173 174 -CONECT 173 172 +CONECT 172 166 173 173 174 +CONECT 173 172 172 CONECT 174 172 175 176 CONECT 175 174 CONECT 176 174 177 178 182 @@ -400,8 +400,8 @@ CONECT 178 176 179 180 181 CONECT 179 178 CONECT 180 178 CONECT 181 178 -CONECT 182 176 183 184 -CONECT 183 182 +CONECT 182 176 183 183 184 +CONECT 183 182 182 CONECT 184 182 185 186 CONECT 185 184 CONECT 186 184 187 188 192 @@ -410,8 +410,8 @@ CONECT 188 186 189 190 191 CONECT 189 188 CONECT 190 188 CONECT 191 188 -CONECT 192 186 193 194 -CONECT 193 192 +CONECT 192 186 193 193 194 +CONECT 193 192 192 CONECT 194 192 195 196 CONECT 195 194 CONECT 196 194 197 198 202 @@ -420,8 +420,8 @@ CONECT 198 196 199 200 201 CONECT 199 198 CONECT 200 198 CONECT 201 198 -CONECT 202 196 203 204 -CONECT 203 202 +CONECT 202 196 203 203 204 +CONECT 203 202 202 CONECT 204 202 205 206 CONECT 205 204 CONECT 206 204 207 208 212 @@ -430,8 +430,8 @@ CONECT 208 206 209 210 211 CONECT 209 208 CONECT 210 208 CONECT 211 208 -CONECT 212 206 213 214 -CONECT 213 212 +CONECT 212 206 213 213 214 +CONECT 213 212 212 CONECT 214 212 215 216 CONECT 215 214 CONECT 216 214 217 218 219 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/output_files/applied_composition.pdb b/unittests/output_files/applied_composition.pdb index 5233f7a..2615b60 100644 --- a/unittests/output_files/applied_composition.pdb +++ b/unittests/output_files/applied_composition.pdb @@ -210,22 +210,22 @@ CONECT 1 2 CONECT 2 1 3 4 5 CONECT 3 2 CONECT 4 2 -CONECT 5 2 6 7 -CONECT 6 5 +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 14 -CONECT 13 12 +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 21 -CONECT 20 19 +CONECT 19 16 20 20 21 +CONECT 20 19 19 CONECT 21 19 22 23 CONECT 22 21 CONECT 23 21 24 25 29 @@ -234,8 +234,8 @@ CONECT 25 23 26 27 28 CONECT 26 25 CONECT 27 25 CONECT 28 25 -CONECT 29 23 30 31 -CONECT 30 29 +CONECT 29 23 30 30 31 +CONECT 30 29 29 CONECT 31 29 32 33 CONECT 32 31 CONECT 33 31 34 35 39 @@ -244,8 +244,8 @@ CONECT 35 33 36 37 38 CONECT 36 35 CONECT 37 35 CONECT 38 35 -CONECT 39 33 40 41 -CONECT 40 39 +CONECT 39 33 40 40 41 +CONECT 40 39 39 CONECT 41 39 42 43 CONECT 42 41 CONECT 43 41 44 45 49 @@ -254,8 +254,8 @@ CONECT 45 43 46 47 48 CONECT 46 45 CONECT 47 45 CONECT 48 45 -CONECT 49 43 50 51 -CONECT 50 49 +CONECT 49 43 50 50 51 +CONECT 50 49 49 CONECT 51 49 52 53 CONECT 52 51 CONECT 53 51 54 55 59 @@ -264,8 +264,8 @@ CONECT 55 53 56 57 58 CONECT 56 55 CONECT 57 55 CONECT 58 55 -CONECT 59 53 60 61 -CONECT 60 59 +CONECT 59 53 60 60 61 +CONECT 60 59 59 CONECT 61 59 62 63 CONECT 62 61 CONECT 63 61 64 65 69 @@ -274,8 +274,8 @@ CONECT 65 63 66 67 68 CONECT 66 65 CONECT 67 65 CONECT 68 65 -CONECT 69 63 70 71 -CONECT 70 69 +CONECT 69 63 70 70 71 +CONECT 70 69 69 CONECT 71 69 72 73 CONECT 72 71 CONECT 73 71 74 75 79 @@ -284,8 +284,8 @@ CONECT 75 73 76 77 78 CONECT 76 75 CONECT 77 75 CONECT 78 75 -CONECT 79 73 80 81 -CONECT 80 79 +CONECT 79 73 80 80 81 +CONECT 80 79 79 CONECT 81 79 82 83 CONECT 82 81 CONECT 83 81 84 85 89 @@ -294,8 +294,8 @@ CONECT 85 83 86 87 88 CONECT 86 85 CONECT 87 85 CONECT 88 85 -CONECT 89 83 90 91 -CONECT 90 89 +CONECT 89 83 90 90 91 +CONECT 90 89 89 CONECT 91 89 92 93 CONECT 92 91 CONECT 93 91 94 95 99 @@ -304,8 +304,8 @@ CONECT 95 93 96 97 98 CONECT 96 95 CONECT 97 95 CONECT 98 95 -CONECT 99 93 100 101 -CONECT 100 99 +CONECT 99 93 100 100 101 +CONECT 100 99 99 CONECT 101 99 102 103 CONECT 102 101 CONECT 103 101 104 105 109 @@ -314,8 +314,8 @@ CONECT 105 103 106 107 108 CONECT 106 105 CONECT 107 105 CONECT 108 105 -CONECT 109 103 110 111 -CONECT 110 109 +CONECT 109 103 110 110 111 +CONECT 110 109 109 CONECT 111 109 112 113 CONECT 112 111 CONECT 113 111 114 115 119 @@ -324,8 +324,8 @@ CONECT 115 113 116 117 118 CONECT 116 115 CONECT 117 115 CONECT 118 115 -CONECT 119 113 120 121 -CONECT 120 119 +CONECT 119 113 120 120 121 +CONECT 120 119 119 CONECT 121 119 122 123 CONECT 122 121 CONECT 123 121 124 125 129 @@ -334,8 +334,8 @@ CONECT 125 123 126 127 128 CONECT 126 125 CONECT 127 125 CONECT 128 125 -CONECT 129 123 130 131 -CONECT 130 129 +CONECT 129 123 130 130 131 +CONECT 130 129 129 CONECT 131 129 132 133 CONECT 132 131 CONECT 133 131 134 135 139 @@ -344,8 +344,8 @@ CONECT 135 133 136 137 138 CONECT 136 135 CONECT 137 135 CONECT 138 135 -CONECT 139 133 140 141 -CONECT 140 139 +CONECT 139 133 140 140 141 +CONECT 140 139 139 CONECT 141 139 142 143 CONECT 142 141 CONECT 143 141 144 145 149 @@ -354,8 +354,8 @@ CONECT 145 143 146 147 148 CONECT 146 145 CONECT 147 145 CONECT 148 145 -CONECT 149 143 150 151 -CONECT 150 149 +CONECT 149 143 150 150 151 +CONECT 150 149 149 CONECT 151 149 152 153 CONECT 152 151 CONECT 153 151 154 155 159 @@ -364,8 +364,8 @@ CONECT 155 153 156 157 158 CONECT 156 155 CONECT 157 155 CONECT 158 155 -CONECT 159 153 160 161 -CONECT 160 159 +CONECT 159 153 160 160 161 +CONECT 160 159 159 CONECT 161 159 162 163 CONECT 162 161 CONECT 163 161 164 165 169 @@ -374,8 +374,8 @@ CONECT 165 163 166 167 168 CONECT 166 165 CONECT 167 165 CONECT 168 165 -CONECT 169 163 170 171 -CONECT 170 169 +CONECT 169 163 170 170 171 +CONECT 170 169 169 CONECT 171 169 172 173 CONECT 172 171 CONECT 173 171 174 175 179 @@ -384,8 +384,8 @@ CONECT 175 173 176 177 178 CONECT 176 175 CONECT 177 175 CONECT 178 175 -CONECT 179 173 180 181 -CONECT 180 179 +CONECT 179 173 180 180 181 +CONECT 180 179 179 CONECT 181 179 182 183 CONECT 182 181 CONECT 183 181 184 185 189 @@ -394,8 +394,8 @@ CONECT 185 183 186 187 188 CONECT 186 185 CONECT 187 185 CONECT 188 185 -CONECT 189 183 190 191 -CONECT 190 189 +CONECT 189 183 190 190 191 +CONECT 190 189 189 CONECT 191 189 192 193 CONECT 192 191 CONECT 193 191 194 195 199 @@ -404,8 +404,8 @@ CONECT 195 193 196 197 198 CONECT 196 195 CONECT 197 195 CONECT 198 195 -CONECT 199 193 200 201 -CONECT 200 199 +CONECT 199 193 200 200 201 +CONECT 200 199 199 CONECT 201 199 202 203 CONECT 202 201 CONECT 203 201 204 205 206 diff --git a/unittests/output_files/leap.log b/unittests/output_files/leap.log index c39cfe6..17223dd 100644 --- a/unittests/output_files/leap.log +++ b/unittests/output_files/leap.log @@ -344338,3 +344338,372735 @@ Marking per-residue atom chain types. 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue 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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/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: 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: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +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: 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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: 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: 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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: Note. +Ignoring 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 index ae067fc..20a1049 100644 --- a/unittests/output_files/mol.pdb +++ b/unittests/output_files/mol.pdb @@ -1,5 +1,5 @@ COMPND MET -AUTHOR GENERATED BY OPEN BABEL 2.4.1 +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 @@ -23,17 +23,17 @@ 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 21.318 26.610 21.383 1.00 0.00 H -ATOM 25 HB3 HIP A 2 20.066 27.157 20.243 1.00 0.00 H -ATOM 26 CG HIP A 2 21.914 26.698 19.383 1.00 0.00 C -ATOM 27 ND1 HIP A 2 23.187 26.196 19.539 1.00 0.00 N -ATOM 28 HD1 HIP A 2 23.686 26.156 20.416 1.00 0.00 H -ATOM 29 CE1 HIP A 2 23.641 25.784 18.368 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 26.000 17.459 1.00 0.00 N -ATOM 32 HE2 HIP A 2 22.778 25.785 16.475 1.00 0.00 H -ATOM 33 CD2 HIP A 2 21.619 26.571 18.067 1.00 0.00 C -ATOM 34 HD2 HIP A 2 20.738 26.828 17.478 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 @@ -253,8 +253,8 @@ 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 O -ATOM 255 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O +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 @@ -310,8 +310,8 @@ 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 O -ATOM 312 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O +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 @@ -348,8 +348,8 @@ 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 O -ATOM 350 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O +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 @@ -407,8 +407,8 @@ 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 O -ATOM 409 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O +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 @@ -561,8 +561,8 @@ 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 O -ATOM 563 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O +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 @@ -610,8 +610,8 @@ 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 O -ATOM 612 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O +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 @@ -632,8 +632,8 @@ 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 O -ATOM 634 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O +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 @@ -703,8 +703,8 @@ 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 O -ATOM 705 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O +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 @@ -715,8 +715,8 @@ 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 O -ATOM 717 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O +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 @@ -854,11 +854,11 @@ 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 O -ATOM 856 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O +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 O -ATOM 859 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O +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 @@ -876,26 +876,26 @@ CONECT 14 13 15 16 17 CONECT 15 14 CONECT 16 14 CONECT 17 14 -CONECT 18 5 19 20 -CONECT 19 18 +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 24 25 26 22 +CONECT 23 22 24 25 26 CONECT 24 23 CONECT 25 23 -CONECT 26 23 27 33 +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 31 34 +CONECT 33 26 26 31 34 CONECT 34 33 CONECT 35 22 -CONECT 36 22 37 38 -CONECT 37 36 +CONECT 36 22 37 37 38 +CONECT 37 36 36 CONECT 38 36 39 40 CONECT 39 38 CONECT 40 38 41 42 57 @@ -903,20 +903,20 @@ CONECT 41 40 CONECT 42 40 43 44 45 CONECT 43 42 CONECT 44 42 -CONECT 45 42 46 55 -CONECT 46 45 47 48 +CONECT 45 42 46 46 55 +CONECT 46 45 45 47 48 CONECT 47 46 -CONECT 48 46 49 50 +CONECT 48 46 49 50 50 CONECT 49 48 -CONECT 50 48 51 53 +CONECT 50 48 48 51 53 CONECT 51 50 52 CONECT 52 51 -CONECT 53 50 54 55 +CONECT 53 50 54 55 55 CONECT 54 53 -CONECT 55 45 53 56 +CONECT 55 45 53 53 56 CONECT 56 55 -CONECT 57 40 58 59 -CONECT 58 57 +CONECT 57 40 58 58 59 +CONECT 58 57 57 CONECT 59 57 60 61 CONECT 60 59 CONECT 61 59 62 63 79 @@ -937,8 +937,8 @@ CONECT 75 72 76 77 78 CONECT 76 75 CONECT 77 75 CONECT 78 75 -CONECT 79 61 80 81 -CONECT 80 79 +CONECT 79 61 80 80 81 +CONECT 80 79 79 CONECT 81 79 82 83 CONECT 82 81 CONECT 83 81 84 85 98 @@ -956,8 +956,8 @@ CONECT 94 88 95 96 97 CONECT 95 94 CONECT 96 94 CONECT 97 94 -CONECT 98 83 99 100 -CONECT 99 98 +CONECT 98 83 99 99 100 +CONECT 99 98 98 CONECT 100 98 101 102 CONECT 101 100 CONECT 102 100 103 104 117 @@ -975,8 +975,8 @@ CONECT 113 110 114 115 116 CONECT 114 113 CONECT 115 113 CONECT 116 113 -CONECT 117 102 118 119 -CONECT 118 117 +CONECT 117 102 118 118 119 +CONECT 118 117 117 CONECT 119 117 120 121 CONECT 120 119 CONECT 121 119 122 123 136 @@ -994,8 +994,8 @@ CONECT 132 126 133 134 135 CONECT 133 132 CONECT 134 132 CONECT 135 132 -CONECT 136 121 137 138 -CONECT 137 136 +CONECT 136 121 137 137 138 +CONECT 137 136 136 CONECT 138 136 139 140 CONECT 139 138 CONECT 140 138 141 142 150 @@ -1003,20 +1003,20 @@ CONECT 141 140 CONECT 142 140 143 144 145 CONECT 143 142 CONECT 144 142 -CONECT 145 142 146 147 -CONECT 146 145 +CONECT 145 142 146 146 147 +CONECT 146 145 145 CONECT 147 145 148 149 CONECT 148 147 CONECT 149 147 -CONECT 150 140 151 152 -CONECT 151 150 +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 157 154 158 159 -CONECT 158 157 +CONECT 157 154 158 158 159 +CONECT 158 157 157 CONECT 159 157 160 161 CONECT 160 159 CONECT 161 159 162 163 179 @@ -1037,8 +1037,8 @@ CONECT 175 172 176 177 178 CONECT 176 175 CONECT 177 175 CONECT 178 175 -CONECT 179 161 180 181 -CONECT 180 179 +CONECT 179 161 180 180 181 +CONECT 180 179 179 CONECT 181 179 182 183 CONECT 182 181 CONECT 183 181 184 185 193 @@ -1051,8 +1051,8 @@ CONECT 189 187 CONECT 190 187 CONECT 191 185 192 CONECT 192 191 -CONECT 193 183 194 195 -CONECT 194 193 +CONECT 193 183 194 194 195 +CONECT 194 193 193 CONECT 195 193 196 197 CONECT 196 195 CONECT 197 195 198 199 212 @@ -1070,8 +1070,8 @@ CONECT 208 202 209 210 211 CONECT 209 208 CONECT 210 208 CONECT 211 208 -CONECT 212 197 213 214 -CONECT 213 212 +CONECT 212 197 213 213 214 +CONECT 213 212 212 CONECT 214 212 215 216 CONECT 215 214 CONECT 216 214 217 218 234 @@ -1092,15 +1092,15 @@ CONECT 230 227 231 232 233 CONECT 231 230 CONECT 232 230 CONECT 233 230 -CONECT 234 216 235 236 -CONECT 235 234 +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 241 238 242 243 -CONECT 242 241 +CONECT 241 238 242 242 243 +CONECT 242 241 241 CONECT 243 241 244 245 CONECT 244 243 CONECT 245 243 246 247 256 @@ -1111,11 +1111,11 @@ CONECT 249 247 CONECT 250 247 251 252 253 CONECT 251 250 CONECT 252 250 -CONECT 253 250 254 255 -CONECT 254 253 +CONECT 253 250 254 254 255 +CONECT 254 253 253 CONECT 255 253 -CONECT 256 245 257 258 -CONECT 257 256 +CONECT 256 245 257 257 258 +CONECT 257 256 256 CONECT 258 256 259 260 CONECT 259 258 CONECT 260 258 261 262 270 @@ -1128,8 +1128,8 @@ CONECT 266 264 CONECT 267 264 CONECT 268 262 269 CONECT 269 268 -CONECT 270 260 271 272 -CONECT 271 270 +CONECT 270 260 271 271 272 +CONECT 271 270 270 CONECT 272 270 273 274 CONECT 273 272 CONECT 274 272 275 276 284 @@ -1142,8 +1142,8 @@ CONECT 280 278 CONECT 281 278 CONECT 282 276 283 CONECT 283 282 -CONECT 284 274 285 286 -CONECT 285 284 +CONECT 284 274 285 285 286 +CONECT 285 284 284 CONECT 286 284 287 288 CONECT 287 286 CONECT 288 286 289 290 298 @@ -1156,8 +1156,8 @@ CONECT 294 292 CONECT 295 292 CONECT 296 290 297 CONECT 297 296 -CONECT 298 288 299 300 -CONECT 299 298 +CONECT 298 288 299 299 300 +CONECT 299 298 298 CONECT 300 298 301 302 CONECT 301 300 CONECT 302 300 303 304 313 @@ -1168,11 +1168,11 @@ CONECT 306 304 CONECT 307 304 308 309 310 CONECT 308 307 CONECT 309 307 -CONECT 310 307 311 312 -CONECT 311 310 +CONECT 310 307 311 311 312 +CONECT 311 310 310 CONECT 312 310 -CONECT 313 302 314 315 -CONECT 314 313 +CONECT 313 302 314 314 315 +CONECT 314 313 313 CONECT 315 313 316 317 CONECT 316 315 CONECT 317 315 318 319 323 @@ -1181,8 +1181,8 @@ CONECT 319 317 320 321 322 CONECT 320 319 CONECT 321 319 CONECT 322 319 -CONECT 323 317 324 325 -CONECT 324 323 +CONECT 323 317 324 324 325 +CONECT 324 323 323 CONECT 325 323 326 327 CONECT 326 325 CONECT 327 325 328 329 339 @@ -1197,8 +1197,8 @@ CONECT 335 329 336 337 338 CONECT 336 335 CONECT 337 335 CONECT 338 335 -CONECT 339 327 340 341 -CONECT 340 339 +CONECT 339 327 340 340 341 +CONECT 340 339 339 CONECT 341 339 342 343 CONECT 342 341 CONECT 343 341 344 345 351 @@ -1206,11 +1206,11 @@ CONECT 344 343 CONECT 345 343 346 347 348 CONECT 346 345 CONECT 347 345 -CONECT 348 345 349 350 -CONECT 349 348 +CONECT 348 345 349 349 350 +CONECT 349 348 348 CONECT 350 348 -CONECT 351 343 352 353 -CONECT 352 351 +CONECT 351 343 352 352 353 +CONECT 352 351 351 CONECT 353 351 354 355 CONECT 354 353 CONECT 355 353 356 357 361 @@ -1219,8 +1219,8 @@ CONECT 357 355 358 359 360 CONECT 358 357 CONECT 359 357 CONECT 360 357 -CONECT 361 355 362 363 -CONECT 362 361 +CONECT 361 355 362 362 363 +CONECT 362 361 361 CONECT 363 361 364 365 CONECT 364 363 CONECT 365 363 366 367 371 @@ -1229,8 +1229,8 @@ CONECT 367 365 368 369 370 CONECT 368 367 CONECT 369 367 CONECT 370 367 -CONECT 371 365 372 373 -CONECT 372 371 +CONECT 371 365 372 372 373 +CONECT 372 371 371 CONECT 373 371 374 375 CONECT 374 373 CONECT 375 373 376 377 385 @@ -1243,8 +1243,8 @@ CONECT 381 379 CONECT 382 379 CONECT 383 377 384 CONECT 384 383 -CONECT 385 375 386 387 -CONECT 386 385 +CONECT 385 375 386 386 387 +CONECT 386 385 385 CONECT 387 385 388 389 CONECT 388 387 CONECT 389 387 390 391 395 @@ -1253,8 +1253,8 @@ CONECT 391 389 392 393 394 CONECT 392 391 CONECT 393 391 CONECT 394 391 -CONECT 395 389 396 397 -CONECT 396 395 +CONECT 395 389 396 396 397 +CONECT 396 395 395 CONECT 397 395 398 399 CONECT 398 397 CONECT 399 397 400 401 410 @@ -1265,11 +1265,11 @@ CONECT 403 401 CONECT 404 401 405 406 407 CONECT 405 404 CONECT 406 404 -CONECT 407 404 408 409 -CONECT 408 407 +CONECT 407 404 408 408 409 +CONECT 408 407 407 CONECT 409 407 -CONECT 410 399 411 412 -CONECT 411 410 +CONECT 410 399 411 411 412 +CONECT 411 410 410 CONECT 412 410 413 414 CONECT 413 412 CONECT 414 412 415 416 432 @@ -1290,8 +1290,8 @@ CONECT 428 425 429 430 431 CONECT 429 428 CONECT 430 428 CONECT 431 428 -CONECT 432 414 433 434 -CONECT 433 432 +CONECT 432 414 433 433 434 +CONECT 433 432 432 CONECT 434 432 435 436 CONECT 435 434 CONECT 436 434 437 438 448 @@ -1306,8 +1306,8 @@ CONECT 444 438 445 446 447 CONECT 445 444 CONECT 446 444 CONECT 447 444 -CONECT 448 436 449 450 -CONECT 449 448 +CONECT 448 436 449 449 450 +CONECT 449 448 448 CONECT 450 448 451 452 CONECT 451 450 CONECT 452 450 453 454 468 @@ -1315,19 +1315,19 @@ CONECT 453 452 CONECT 454 452 455 456 457 CONECT 455 454 CONECT 456 454 -CONECT 457 454 458 466 -CONECT 458 457 459 460 +CONECT 457 454 458 458 466 +CONECT 458 457 457 459 460 CONECT 459 458 -CONECT 460 458 461 462 +CONECT 460 458 461 462 462 CONECT 461 460 -CONECT 462 460 463 464 +CONECT 462 460 460 463 464 CONECT 463 462 -CONECT 464 462 465 466 +CONECT 464 462 465 466 466 CONECT 465 464 -CONECT 466 457 464 467 +CONECT 466 457 464 464 467 CONECT 467 466 -CONECT 468 452 469 470 -CONECT 469 468 +CONECT 468 452 469 469 470 +CONECT 469 468 468 CONECT 470 468 471 472 CONECT 471 470 CONECT 472 470 473 474 490 @@ -1348,8 +1348,8 @@ CONECT 486 483 487 488 489 CONECT 487 486 CONECT 488 486 CONECT 489 486 -CONECT 490 472 491 492 -CONECT 491 490 +CONECT 490 472 491 491 492 +CONECT 491 490 490 CONECT 492 490 493 494 CONECT 493 492 CONECT 494 492 495 496 507 @@ -1360,13 +1360,13 @@ CONECT 498 496 CONECT 499 496 500 501 502 CONECT 500 499 CONECT 501 499 -CONECT 502 499 503 504 -CONECT 503 502 +CONECT 502 499 503 503 504 +CONECT 503 502 502 CONECT 504 502 505 506 CONECT 505 504 CONECT 506 504 -CONECT 507 494 508 509 -CONECT 508 507 +CONECT 507 494 508 508 509 +CONECT 508 507 507 CONECT 509 507 510 511 CONECT 510 509 CONECT 511 509 512 513 528 @@ -1374,20 +1374,20 @@ CONECT 512 511 CONECT 513 511 514 515 516 CONECT 514 513 CONECT 515 513 -CONECT 516 513 517 526 -CONECT 517 516 518 519 +CONECT 516 513 517 517 526 +CONECT 517 516 516 518 519 CONECT 518 517 -CONECT 519 517 520 521 +CONECT 519 517 520 521 521 CONECT 520 519 -CONECT 521 519 522 524 +CONECT 521 519 519 522 524 CONECT 522 521 523 CONECT 523 522 -CONECT 524 521 525 526 +CONECT 524 521 525 526 526 CONECT 525 524 -CONECT 526 516 524 527 +CONECT 526 516 524 524 527 CONECT 527 526 -CONECT 528 511 529 530 -CONECT 529 528 +CONECT 528 511 529 529 530 +CONECT 529 528 528 CONECT 530 528 531 532 CONECT 531 530 CONECT 532 530 533 534 538 @@ -1396,8 +1396,8 @@ CONECT 534 532 535 536 537 CONECT 535 534 CONECT 536 534 CONECT 537 534 -CONECT 538 532 539 540 -CONECT 539 538 +CONECT 538 532 539 539 540 +CONECT 539 538 538 CONECT 540 538 541 542 CONECT 541 540 CONECT 542 540 543 544 552 @@ -1405,13 +1405,13 @@ CONECT 543 542 CONECT 544 542 545 546 547 CONECT 545 544 CONECT 546 544 -CONECT 547 544 548 549 -CONECT 548 547 +CONECT 547 544 548 548 549 +CONECT 548 547 547 CONECT 549 547 550 551 CONECT 550 549 CONECT 551 549 -CONECT 552 542 553 554 -CONECT 553 552 +CONECT 552 542 553 553 554 +CONECT 553 552 552 CONECT 554 552 555 556 CONECT 555 554 CONECT 556 554 557 558 564 @@ -1419,11 +1419,11 @@ CONECT 557 556 CONECT 558 556 559 560 561 CONECT 559 558 CONECT 560 558 -CONECT 561 558 562 563 -CONECT 562 561 +CONECT 561 558 562 562 563 +CONECT 562 561 561 CONECT 563 561 -CONECT 564 556 565 566 -CONECT 565 564 +CONECT 564 556 565 565 566 +CONECT 565 564 564 CONECT 566 564 567 568 CONECT 567 566 CONECT 568 566 569 570 578 @@ -1431,20 +1431,20 @@ CONECT 569 568 CONECT 570 568 571 572 573 CONECT 571 570 CONECT 572 570 -CONECT 573 570 574 575 -CONECT 574 573 +CONECT 573 570 574 574 575 +CONECT 574 573 573 CONECT 575 573 576 577 CONECT 576 575 CONECT 577 575 -CONECT 578 568 579 580 -CONECT 579 578 +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 585 582 586 587 -CONECT 586 585 +CONECT 585 582 586 586 587 +CONECT 586 585 585 CONECT 587 585 588 589 CONECT 588 587 CONECT 589 587 590 591 601 @@ -1459,8 +1459,8 @@ CONECT 597 591 598 599 600 CONECT 598 597 CONECT 599 597 CONECT 600 597 -CONECT 601 589 602 603 -CONECT 602 601 +CONECT 601 589 602 602 603 +CONECT 602 601 601 CONECT 603 601 604 605 CONECT 604 603 CONECT 605 603 606 607 613 @@ -1468,18 +1468,18 @@ CONECT 606 605 CONECT 607 605 608 609 610 CONECT 608 607 CONECT 609 607 -CONECT 610 607 611 612 -CONECT 611 610 +CONECT 610 607 611 611 612 +CONECT 611 610 610 CONECT 612 610 -CONECT 613 605 614 615 -CONECT 614 613 +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 620 617 621 622 -CONECT 621 620 +CONECT 620 617 621 621 622 +CONECT 621 620 620 CONECT 622 620 623 624 CONECT 623 622 CONECT 624 622 625 626 635 @@ -1490,11 +1490,11 @@ CONECT 628 626 CONECT 629 626 630 631 632 CONECT 630 629 CONECT 631 629 -CONECT 632 629 633 634 -CONECT 633 632 +CONECT 632 629 633 633 634 +CONECT 633 632 632 CONECT 634 632 -CONECT 635 624 636 637 -CONECT 636 635 +CONECT 635 624 636 636 637 +CONECT 636 635 635 CONECT 637 635 638 639 CONECT 638 637 CONECT 639 637 640 641 659 @@ -1502,23 +1502,23 @@ CONECT 640 639 CONECT 641 639 642 643 644 CONECT 642 641 CONECT 643 641 -CONECT 644 641 645 658 -CONECT 645 644 646 647 +CONECT 644 641 645 645 658 +CONECT 645 644 644 646 647 CONECT 646 645 CONECT 647 645 648 649 CONECT 648 647 -CONECT 649 647 650 658 -CONECT 650 649 651 652 +CONECT 649 647 650 650 658 +CONECT 650 649 649 651 652 CONECT 651 650 -CONECT 652 650 653 654 +CONECT 652 650 653 654 654 CONECT 653 652 -CONECT 654 652 655 656 +CONECT 654 652 652 655 656 CONECT 655 654 -CONECT 656 654 657 658 +CONECT 656 654 657 658 658 CONECT 657 656 -CONECT 658 644 649 656 -CONECT 659 639 660 661 -CONECT 660 659 +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 @@ -1531,8 +1531,8 @@ CONECT 669 667 CONECT 670 667 CONECT 671 665 672 CONECT 672 671 -CONECT 673 663 674 675 -CONECT 674 673 +CONECT 673 663 674 674 675 +CONECT 674 673 673 CONECT 675 673 676 677 CONECT 676 675 CONECT 677 675 678 679 694 @@ -1540,20 +1540,20 @@ CONECT 678 677 CONECT 679 677 680 681 682 CONECT 680 679 CONECT 681 679 -CONECT 682 679 683 692 -CONECT 683 682 684 685 +CONECT 682 679 683 683 692 +CONECT 683 682 682 684 685 CONECT 684 683 -CONECT 685 683 686 687 +CONECT 685 683 686 687 687 CONECT 686 685 -CONECT 687 685 688 690 +CONECT 687 685 685 688 690 CONECT 688 687 689 CONECT 689 688 -CONECT 690 687 691 692 +CONECT 690 687 691 692 692 CONECT 691 690 -CONECT 692 682 690 693 +CONECT 692 682 690 690 693 CONECT 693 692 -CONECT 694 677 695 696 -CONECT 695 694 +CONECT 694 677 695 695 696 +CONECT 695 694 694 CONECT 696 694 697 698 CONECT 697 696 CONECT 698 696 699 700 706 @@ -1561,11 +1561,11 @@ CONECT 699 698 CONECT 700 698 701 702 703 CONECT 701 700 CONECT 702 700 -CONECT 703 700 704 705 -CONECT 704 703 +CONECT 703 700 704 704 705 +CONECT 704 703 703 CONECT 705 703 -CONECT 706 698 707 708 -CONECT 707 706 +CONECT 706 698 707 707 708 +CONECT 707 706 706 CONECT 708 706 709 710 CONECT 709 708 CONECT 710 708 711 712 718 @@ -1573,11 +1573,11 @@ CONECT 711 710 CONECT 712 710 713 714 715 CONECT 713 712 CONECT 714 712 -CONECT 715 712 716 717 -CONECT 716 715 +CONECT 715 712 716 716 717 +CONECT 716 715 715 CONECT 717 715 -CONECT 718 710 719 720 -CONECT 719 718 +CONECT 718 710 719 719 720 +CONECT 719 718 718 CONECT 720 718 721 722 CONECT 721 720 CONECT 722 720 723 724 728 @@ -1586,8 +1586,8 @@ CONECT 724 722 725 726 727 CONECT 725 724 CONECT 726 724 CONECT 727 724 -CONECT 728 722 729 730 -CONECT 729 728 +CONECT 728 722 729 729 730 +CONECT 729 728 728 CONECT 730 728 731 732 CONECT 731 730 CONECT 732 730 733 734 742 @@ -1600,8 +1600,8 @@ CONECT 738 736 CONECT 739 736 CONECT 740 734 741 CONECT 741 740 -CONECT 742 732 743 744 -CONECT 743 742 +CONECT 742 732 743 743 744 +CONECT 743 742 742 CONECT 744 742 745 746 CONECT 745 744 CONECT 746 744 747 748 764 @@ -1622,8 +1622,8 @@ CONECT 760 757 761 762 763 CONECT 761 760 CONECT 762 760 CONECT 763 760 -CONECT 764 746 765 766 -CONECT 765 764 +CONECT 764 746 765 765 766 +CONECT 765 764 764 CONECT 766 764 767 768 CONECT 767 766 CONECT 768 766 769 770 778 @@ -1636,8 +1636,8 @@ CONECT 774 772 CONECT 775 772 CONECT 776 770 777 CONECT 777 776 -CONECT 778 768 779 780 -CONECT 779 778 +CONECT 778 768 779 779 780 +CONECT 779 778 778 CONECT 780 778 781 782 CONECT 781 780 CONECT 782 780 783 784 798 @@ -1645,19 +1645,19 @@ CONECT 783 782 CONECT 784 782 785 786 787 CONECT 785 784 CONECT 786 784 -CONECT 787 784 788 796 -CONECT 788 787 789 790 +CONECT 787 784 788 788 796 +CONECT 788 787 787 789 790 CONECT 789 788 -CONECT 790 788 791 792 +CONECT 790 788 791 792 792 CONECT 791 790 -CONECT 792 790 793 794 +CONECT 792 790 790 793 794 CONECT 793 792 -CONECT 794 792 795 796 +CONECT 794 792 795 796 796 CONECT 795 794 -CONECT 796 787 794 797 +CONECT 796 787 794 794 797 CONECT 797 796 -CONECT 798 782 799 800 -CONECT 799 798 +CONECT 798 782 799 799 800 +CONECT 799 798 798 CONECT 800 798 801 802 CONECT 801 800 CONECT 802 800 803 804 812 @@ -1670,8 +1670,8 @@ CONECT 808 806 CONECT 809 806 CONECT 810 804 811 CONECT 811 810 -CONECT 812 802 813 814 -CONECT 813 812 +CONECT 812 802 813 813 814 +CONECT 813 812 812 CONECT 814 812 815 816 CONECT 815 814 CONECT 816 814 817 818 828 @@ -1686,8 +1686,8 @@ CONECT 824 818 825 826 827 CONECT 825 824 CONECT 826 824 CONECT 827 824 -CONECT 828 816 829 830 -CONECT 829 828 +CONECT 828 816 829 829 830 +CONECT 829 828 828 CONECT 830 828 831 832 CONECT 831 830 CONECT 832 830 833 834 842 @@ -1700,8 +1700,8 @@ CONECT 838 836 CONECT 839 836 CONECT 840 834 841 CONECT 841 840 -CONECT 842 832 843 844 -CONECT 843 842 +CONECT 842 832 843 843 844 +CONECT 843 842 842 CONECT 844 842 845 846 CONECT 845 844 CONECT 846 844 847 848 857 @@ -1712,11 +1712,11 @@ CONECT 850 848 CONECT 851 848 852 853 854 CONECT 852 851 CONECT 853 851 -CONECT 854 851 855 856 -CONECT 855 854 +CONECT 854 851 855 855 856 +CONECT 855 854 854 CONECT 856 854 -CONECT 857 846 858 859 -CONECT 858 857 +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/mol.prmtop b/unittests/output_files/mol.prmtop index 4d8c5e6..293db86 100644 --- a/unittests/output_files/mol.prmtop +++ b/unittests/output_files/mol.prmtop @@ -1,11 +1,11 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 10/14/20 10:16:23 +%VERSION VERSION_STAMP = V0001.000 DATE = 11/05/20 16:13:52 %FLAG TITLE %FORMAT(20a4) default_name %FLAG POINTERS %FORMAT(10I8) - 859 14 420 446 954 605 1919 1468 0 0 - 4720 56 446 605 1468 40 93 40 25 0 + 859 14 420 446 954 605 1919 1470 0 0 + 4720 56 446 605 1470 40 93 41 25 0 0 0 0 0 0 0 0 0 24 0 0 %FLAG ATOM_NAME @@ -772,6 +772,7 @@ GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE THR VAL THR GLU 1.60000000E-01 2.00000000E-01 2.50000000E-01 1.80000000E-01 2.50000000E-01 0.00000000E+00 1.66666667E-01 3.00000000E+00 3.50000000E+00 1.52500000E+00 6.52500000E+00 1.67500000E+00 1.05000000E+01 1.10000000E+00 1.00000000E+00 + 0.00000000E+00 %FLAG DIHEDRAL_PERIODICITY %FORMAT(5E16.8) 1.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 3.00000000E+00 @@ -782,6 +783,7 @@ GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE THR VAL THR GLU 3.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00 3.00000000E+00 3.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 %FLAG DIHEDRAL_PHASE %FORMAT(5E16.8) 0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 @@ -792,6 +794,7 @@ GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE THR VAL THR GLU 0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 + 3.14159400E+00 %FLAG SCEE_SCALE_FACTOR %FORMAT(5E16.8) 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 @@ -802,6 +805,7 @@ GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE THR VAL THR GLU 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 %FLAG SCNB_SCALE_FACTOR %FORMAT(5E16.8) 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 @@ -812,6 +816,7 @@ GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE THR VAL THR GLU 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 %FLAG SOLTY %FORMAT(5E16.8) 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 @@ -3445,6 +3450,7 @@ GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE THR VAL THR GLU 1812 1842 -1836 -1839 38 1818 1830 -1827 -1833 38 1848 1863 -1857 -1860 38 1869 1908 -1902 -1905 38 1884 1896 -1893 -1899 38 1914 1980 -1974 -1977 38 + 1929 1944 -1971 -1965 41 1938 1947 -1944 -1971 41 1971 1920 -1929 -1932 39 1986 2022 -2016 -2019 38 2028 2085 -2079 -2082 38 2052 2067 -2058 -2061 39 2046 2073 -2043 -2034 39 2091 2121 -2115 -2118 38 diff --git a/unittests/output_files/test_gly_to_K.pdb b/unittests/output_files/test_gly_to_K.pdb index e285e22..9460924 100644 --- a/unittests/output_files/test_gly_to_K.pdb +++ b/unittests/output_files/test_gly_to_K.pdb @@ -1,5 +1,5 @@ COMPND MET -AUTHOR GENERATED BY OPEN BABEL 2.4.1 +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 @@ -151,9 +151,9 @@ 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 38.860 25.169 36.064 1.00 0.00 H -ATOM 153 HB2 A01 A 9 38.636 23.507 36.663 1.00 0.00 H -ATOM 154 HB3 A01 A 9 40.161 24.369 36.976 1.00 0.00 H +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 @@ -252,8 +252,8 @@ 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 O -ATOM 254 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O +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 @@ -309,8 +309,8 @@ 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 O -ATOM 311 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O +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 @@ -347,8 +347,8 @@ 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 O -ATOM 349 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O +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 @@ -406,8 +406,8 @@ 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 O -ATOM 408 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O +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 @@ -560,8 +560,8 @@ 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 O -ATOM 562 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O +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 @@ -609,8 +609,8 @@ 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 O -ATOM 611 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O +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 @@ -631,8 +631,8 @@ 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 O -ATOM 633 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O +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 @@ -702,8 +702,8 @@ 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 O -ATOM 704 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O +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 @@ -714,8 +714,8 @@ 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 O -ATOM 716 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O +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 @@ -853,11 +853,11 @@ 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 O -ATOM 855 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O +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 O -ATOM 858 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O +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 @@ -875,8 +875,8 @@ CONECT 14 13 15 16 17 CONECT 15 14 CONECT 16 14 CONECT 17 14 -CONECT 18 5 19 20 -CONECT 19 18 +CONECT 18 5 19 19 20 +CONECT 19 18 18 CONECT 20 18 21 22 CONECT 21 20 CONECT 22 20 23 24 32 @@ -889,8 +889,8 @@ CONECT 28 26 CONECT 29 26 CONECT 30 24 31 CONECT 31 30 -CONECT 32 22 33 34 -CONECT 33 32 +CONECT 32 22 33 33 34 +CONECT 33 32 32 CONECT 34 32 35 36 CONECT 35 34 CONECT 36 34 37 38 53 @@ -898,20 +898,20 @@ 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 41 38 42 42 51 +CONECT 42 41 41 43 44 CONECT 43 42 -CONECT 44 42 45 46 +CONECT 44 42 45 46 46 CONECT 45 44 -CONECT 46 44 47 49 +CONECT 46 44 44 47 49 CONECT 47 46 48 CONECT 48 47 -CONECT 49 46 50 51 +CONECT 49 46 50 51 51 CONECT 50 49 -CONECT 51 41 49 52 +CONECT 51 41 49 49 52 CONECT 52 51 -CONECT 53 36 54 55 -CONECT 54 53 +CONECT 53 36 54 54 55 +CONECT 54 53 53 CONECT 55 53 56 57 CONECT 56 55 CONECT 57 55 58 59 75 @@ -932,8 +932,8 @@ CONECT 71 68 72 73 74 CONECT 72 71 CONECT 73 71 CONECT 74 71 -CONECT 75 57 76 77 -CONECT 76 75 +CONECT 75 57 76 76 77 +CONECT 76 75 75 CONECT 77 75 78 79 CONECT 78 77 CONECT 79 77 80 81 94 @@ -951,8 +951,8 @@ CONECT 90 84 91 92 93 CONECT 91 90 CONECT 92 90 CONECT 93 90 -CONECT 94 79 95 96 -CONECT 95 94 +CONECT 94 79 95 95 96 +CONECT 95 94 94 CONECT 96 94 97 98 CONECT 97 96 CONECT 98 96 99 100 113 @@ -970,8 +970,8 @@ CONECT 109 106 110 111 112 CONECT 110 109 CONECT 111 109 CONECT 112 109 -CONECT 113 98 114 115 -CONECT 114 113 +CONECT 113 98 114 114 115 +CONECT 114 113 113 CONECT 115 113 116 117 CONECT 116 115 CONECT 117 115 118 119 132 @@ -989,8 +989,8 @@ CONECT 128 122 129 130 131 CONECT 129 128 CONECT 130 128 CONECT 131 128 -CONECT 132 117 133 134 -CONECT 133 132 +CONECT 132 117 133 133 134 +CONECT 133 132 132 CONECT 134 132 135 136 CONECT 135 134 CONECT 136 134 137 138 146 @@ -998,23 +998,23 @@ CONECT 137 136 CONECT 138 136 139 140 141 CONECT 139 138 CONECT 140 138 -CONECT 141 138 142 143 -CONECT 142 141 +CONECT 141 138 142 142 143 +CONECT 142 141 141 CONECT 143 141 144 145 CONECT 144 143 CONECT 145 143 -CONECT 146 136 147 148 -CONECT 147 146 +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 151 152 153 154 150 +CONECT 151 150 152 153 154 CONECT 152 151 CONECT 153 151 CONECT 154 151 CONECT 155 150 -CONECT 156 150 157 158 -CONECT 157 156 +CONECT 156 150 157 157 158 +CONECT 157 156 156 CONECT 158 156 159 160 CONECT 159 158 CONECT 160 158 161 162 178 @@ -1035,8 +1035,8 @@ CONECT 174 171 175 176 177 CONECT 175 174 CONECT 176 174 CONECT 177 174 -CONECT 178 160 179 180 -CONECT 179 178 +CONECT 178 160 179 179 180 +CONECT 179 178 178 CONECT 180 178 181 182 CONECT 181 180 CONECT 182 180 183 184 192 @@ -1049,8 +1049,8 @@ CONECT 188 186 CONECT 189 186 CONECT 190 184 191 CONECT 191 190 -CONECT 192 182 193 194 -CONECT 193 192 +CONECT 192 182 193 193 194 +CONECT 193 192 192 CONECT 194 192 195 196 CONECT 195 194 CONECT 196 194 197 198 211 @@ -1068,8 +1068,8 @@ CONECT 207 201 208 209 210 CONECT 208 207 CONECT 209 207 CONECT 210 207 -CONECT 211 196 212 213 -CONECT 212 211 +CONECT 211 196 212 212 213 +CONECT 212 211 211 CONECT 213 211 214 215 CONECT 214 213 CONECT 215 213 216 217 233 @@ -1090,15 +1090,15 @@ CONECT 229 226 230 231 232 CONECT 230 229 CONECT 231 229 CONECT 232 229 -CONECT 233 215 234 235 -CONECT 234 233 +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 240 237 241 242 -CONECT 241 240 +CONECT 240 237 241 241 242 +CONECT 241 240 240 CONECT 242 240 243 244 CONECT 243 242 CONECT 244 242 245 246 255 @@ -1109,11 +1109,11 @@ CONECT 248 246 CONECT 249 246 250 251 252 CONECT 250 249 CONECT 251 249 -CONECT 252 249 253 254 -CONECT 253 252 +CONECT 252 249 253 253 254 +CONECT 253 252 252 CONECT 254 252 -CONECT 255 244 256 257 -CONECT 256 255 +CONECT 255 244 256 256 257 +CONECT 256 255 255 CONECT 257 255 258 259 CONECT 258 257 CONECT 259 257 260 261 269 @@ -1126,8 +1126,8 @@ CONECT 265 263 CONECT 266 263 CONECT 267 261 268 CONECT 268 267 -CONECT 269 259 270 271 -CONECT 270 269 +CONECT 269 259 270 270 271 +CONECT 270 269 269 CONECT 271 269 272 273 CONECT 272 271 CONECT 273 271 274 275 283 @@ -1140,8 +1140,8 @@ CONECT 279 277 CONECT 280 277 CONECT 281 275 282 CONECT 282 281 -CONECT 283 273 284 285 -CONECT 284 283 +CONECT 283 273 284 284 285 +CONECT 284 283 283 CONECT 285 283 286 287 CONECT 286 285 CONECT 287 285 288 289 297 @@ -1154,8 +1154,8 @@ CONECT 293 291 CONECT 294 291 CONECT 295 289 296 CONECT 296 295 -CONECT 297 287 298 299 -CONECT 298 297 +CONECT 297 287 298 298 299 +CONECT 298 297 297 CONECT 299 297 300 301 CONECT 300 299 CONECT 301 299 302 303 312 @@ -1166,11 +1166,11 @@ CONECT 305 303 CONECT 306 303 307 308 309 CONECT 307 306 CONECT 308 306 -CONECT 309 306 310 311 -CONECT 310 309 +CONECT 309 306 310 310 311 +CONECT 310 309 309 CONECT 311 309 -CONECT 312 301 313 314 -CONECT 313 312 +CONECT 312 301 313 313 314 +CONECT 313 312 312 CONECT 314 312 315 316 CONECT 315 314 CONECT 316 314 317 318 322 @@ -1179,8 +1179,8 @@ CONECT 318 316 319 320 321 CONECT 319 318 CONECT 320 318 CONECT 321 318 -CONECT 322 316 323 324 -CONECT 323 322 +CONECT 322 316 323 323 324 +CONECT 323 322 322 CONECT 324 322 325 326 CONECT 325 324 CONECT 326 324 327 328 338 @@ -1195,8 +1195,8 @@ CONECT 334 328 335 336 337 CONECT 335 334 CONECT 336 334 CONECT 337 334 -CONECT 338 326 339 340 -CONECT 339 338 +CONECT 338 326 339 339 340 +CONECT 339 338 338 CONECT 340 338 341 342 CONECT 341 340 CONECT 342 340 343 344 350 @@ -1204,11 +1204,11 @@ CONECT 343 342 CONECT 344 342 345 346 347 CONECT 345 344 CONECT 346 344 -CONECT 347 344 348 349 -CONECT 348 347 +CONECT 347 344 348 348 349 +CONECT 348 347 347 CONECT 349 347 -CONECT 350 342 351 352 -CONECT 351 350 +CONECT 350 342 351 351 352 +CONECT 351 350 350 CONECT 352 350 353 354 CONECT 353 352 CONECT 354 352 355 356 360 @@ -1217,8 +1217,8 @@ CONECT 356 354 357 358 359 CONECT 357 356 CONECT 358 356 CONECT 359 356 -CONECT 360 354 361 362 -CONECT 361 360 +CONECT 360 354 361 361 362 +CONECT 361 360 360 CONECT 362 360 363 364 CONECT 363 362 CONECT 364 362 365 366 370 @@ -1227,8 +1227,8 @@ CONECT 366 364 367 368 369 CONECT 367 366 CONECT 368 366 CONECT 369 366 -CONECT 370 364 371 372 -CONECT 371 370 +CONECT 370 364 371 371 372 +CONECT 371 370 370 CONECT 372 370 373 374 CONECT 373 372 CONECT 374 372 375 376 384 @@ -1241,8 +1241,8 @@ CONECT 380 378 CONECT 381 378 CONECT 382 376 383 CONECT 383 382 -CONECT 384 374 385 386 -CONECT 385 384 +CONECT 384 374 385 385 386 +CONECT 385 384 384 CONECT 386 384 387 388 CONECT 387 386 CONECT 388 386 389 390 394 @@ -1251,8 +1251,8 @@ CONECT 390 388 391 392 393 CONECT 391 390 CONECT 392 390 CONECT 393 390 -CONECT 394 388 395 396 -CONECT 395 394 +CONECT 394 388 395 395 396 +CONECT 395 394 394 CONECT 396 394 397 398 CONECT 397 396 CONECT 398 396 399 400 409 @@ -1263,11 +1263,11 @@ CONECT 402 400 CONECT 403 400 404 405 406 CONECT 404 403 CONECT 405 403 -CONECT 406 403 407 408 -CONECT 407 406 +CONECT 406 403 407 407 408 +CONECT 407 406 406 CONECT 408 406 -CONECT 409 398 410 411 -CONECT 410 409 +CONECT 409 398 410 410 411 +CONECT 410 409 409 CONECT 411 409 412 413 CONECT 412 411 CONECT 413 411 414 415 431 @@ -1288,8 +1288,8 @@ CONECT 427 424 428 429 430 CONECT 428 427 CONECT 429 427 CONECT 430 427 -CONECT 431 413 432 433 -CONECT 432 431 +CONECT 431 413 432 432 433 +CONECT 432 431 431 CONECT 433 431 434 435 CONECT 434 433 CONECT 435 433 436 437 447 @@ -1304,8 +1304,8 @@ CONECT 443 437 444 445 446 CONECT 444 443 CONECT 445 443 CONECT 446 443 -CONECT 447 435 448 449 -CONECT 448 447 +CONECT 447 435 448 448 449 +CONECT 448 447 447 CONECT 449 447 450 451 CONECT 450 449 CONECT 451 449 452 453 467 @@ -1313,19 +1313,19 @@ CONECT 452 451 CONECT 453 451 454 455 456 CONECT 454 453 CONECT 455 453 -CONECT 456 453 457 465 -CONECT 457 456 458 459 +CONECT 456 453 457 457 465 +CONECT 457 456 456 458 459 CONECT 458 457 -CONECT 459 457 460 461 +CONECT 459 457 460 461 461 CONECT 460 459 -CONECT 461 459 462 463 +CONECT 461 459 459 462 463 CONECT 462 461 -CONECT 463 461 464 465 +CONECT 463 461 464 465 465 CONECT 464 463 -CONECT 465 456 463 466 +CONECT 465 456 463 463 466 CONECT 466 465 -CONECT 467 451 468 469 -CONECT 468 467 +CONECT 467 451 468 468 469 +CONECT 468 467 467 CONECT 469 467 470 471 CONECT 470 469 CONECT 471 469 472 473 489 @@ -1346,8 +1346,8 @@ CONECT 485 482 486 487 488 CONECT 486 485 CONECT 487 485 CONECT 488 485 -CONECT 489 471 490 491 -CONECT 490 489 +CONECT 489 471 490 490 491 +CONECT 490 489 489 CONECT 491 489 492 493 CONECT 492 491 CONECT 493 491 494 495 506 @@ -1358,13 +1358,13 @@ CONECT 497 495 CONECT 498 495 499 500 501 CONECT 499 498 CONECT 500 498 -CONECT 501 498 502 503 -CONECT 502 501 +CONECT 501 498 502 502 503 +CONECT 502 501 501 CONECT 503 501 504 505 CONECT 504 503 CONECT 505 503 -CONECT 506 493 507 508 -CONECT 507 506 +CONECT 506 493 507 507 508 +CONECT 507 506 506 CONECT 508 506 509 510 CONECT 509 508 CONECT 510 508 511 512 527 @@ -1372,20 +1372,20 @@ CONECT 511 510 CONECT 512 510 513 514 515 CONECT 513 512 CONECT 514 512 -CONECT 515 512 516 525 -CONECT 516 515 517 518 +CONECT 515 512 516 516 525 +CONECT 516 515 515 517 518 CONECT 517 516 -CONECT 518 516 519 520 +CONECT 518 516 519 520 520 CONECT 519 518 -CONECT 520 518 521 523 +CONECT 520 518 518 521 523 CONECT 521 520 522 CONECT 522 521 -CONECT 523 520 524 525 +CONECT 523 520 524 525 525 CONECT 524 523 -CONECT 525 515 523 526 +CONECT 525 515 523 523 526 CONECT 526 525 -CONECT 527 510 528 529 -CONECT 528 527 +CONECT 527 510 528 528 529 +CONECT 528 527 527 CONECT 529 527 530 531 CONECT 530 529 CONECT 531 529 532 533 537 @@ -1394,8 +1394,8 @@ CONECT 533 531 534 535 536 CONECT 534 533 CONECT 535 533 CONECT 536 533 -CONECT 537 531 538 539 -CONECT 538 537 +CONECT 537 531 538 538 539 +CONECT 538 537 537 CONECT 539 537 540 541 CONECT 540 539 CONECT 541 539 542 543 551 @@ -1403,13 +1403,13 @@ CONECT 542 541 CONECT 543 541 544 545 546 CONECT 544 543 CONECT 545 543 -CONECT 546 543 547 548 -CONECT 547 546 +CONECT 546 543 547 547 548 +CONECT 547 546 546 CONECT 548 546 549 550 CONECT 549 548 CONECT 550 548 -CONECT 551 541 552 553 -CONECT 552 551 +CONECT 551 541 552 552 553 +CONECT 552 551 551 CONECT 553 551 554 555 CONECT 554 553 CONECT 555 553 556 557 563 @@ -1417,11 +1417,11 @@ CONECT 556 555 CONECT 557 555 558 559 560 CONECT 558 557 CONECT 559 557 -CONECT 560 557 561 562 -CONECT 561 560 +CONECT 560 557 561 561 562 +CONECT 561 560 560 CONECT 562 560 -CONECT 563 555 564 565 -CONECT 564 563 +CONECT 563 555 564 564 565 +CONECT 564 563 563 CONECT 565 563 566 567 CONECT 566 565 CONECT 567 565 568 569 577 @@ -1429,20 +1429,20 @@ CONECT 568 567 CONECT 569 567 570 571 572 CONECT 570 569 CONECT 571 569 -CONECT 572 569 573 574 -CONECT 573 572 +CONECT 572 569 573 573 574 +CONECT 573 572 572 CONECT 574 572 575 576 CONECT 575 574 CONECT 576 574 -CONECT 577 567 578 579 -CONECT 578 577 +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 584 581 585 586 -CONECT 585 584 +CONECT 584 581 585 585 586 +CONECT 585 584 584 CONECT 586 584 587 588 CONECT 587 586 CONECT 588 586 589 590 600 @@ -1457,8 +1457,8 @@ CONECT 596 590 597 598 599 CONECT 597 596 CONECT 598 596 CONECT 599 596 -CONECT 600 588 601 602 -CONECT 601 600 +CONECT 600 588 601 601 602 +CONECT 601 600 600 CONECT 602 600 603 604 CONECT 603 602 CONECT 604 602 605 606 612 @@ -1466,18 +1466,18 @@ CONECT 605 604 CONECT 606 604 607 608 609 CONECT 607 606 CONECT 608 606 -CONECT 609 606 610 611 -CONECT 610 609 +CONECT 609 606 610 610 611 +CONECT 610 609 609 CONECT 611 609 -CONECT 612 604 613 614 -CONECT 613 612 +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 619 616 620 621 -CONECT 620 619 +CONECT 619 616 620 620 621 +CONECT 620 619 619 CONECT 621 619 622 623 CONECT 622 621 CONECT 623 621 624 625 634 @@ -1488,11 +1488,11 @@ CONECT 627 625 CONECT 628 625 629 630 631 CONECT 629 628 CONECT 630 628 -CONECT 631 628 632 633 -CONECT 632 631 +CONECT 631 628 632 632 633 +CONECT 632 631 631 CONECT 633 631 -CONECT 634 623 635 636 -CONECT 635 634 +CONECT 634 623 635 635 636 +CONECT 635 634 634 CONECT 636 634 637 638 CONECT 637 636 CONECT 638 636 639 640 658 @@ -1500,23 +1500,23 @@ CONECT 639 638 CONECT 640 638 641 642 643 CONECT 641 640 CONECT 642 640 -CONECT 643 640 644 657 -CONECT 644 643 645 646 +CONECT 643 640 644 644 657 +CONECT 644 643 643 645 646 CONECT 645 644 CONECT 646 644 647 648 CONECT 647 646 -CONECT 648 646 649 657 -CONECT 649 648 650 651 +CONECT 648 646 649 649 657 +CONECT 649 648 648 650 651 CONECT 650 649 -CONECT 651 649 652 653 +CONECT 651 649 652 653 653 CONECT 652 651 -CONECT 653 651 654 655 +CONECT 653 651 651 654 655 CONECT 654 653 -CONECT 655 653 656 657 +CONECT 655 653 656 657 657 CONECT 656 655 -CONECT 657 643 648 655 -CONECT 658 638 659 660 -CONECT 659 658 +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 @@ -1529,8 +1529,8 @@ CONECT 668 666 CONECT 669 666 CONECT 670 664 671 CONECT 671 670 -CONECT 672 662 673 674 -CONECT 673 672 +CONECT 672 662 673 673 674 +CONECT 673 672 672 CONECT 674 672 675 676 CONECT 675 674 CONECT 676 674 677 678 693 @@ -1538,20 +1538,20 @@ CONECT 677 676 CONECT 678 676 679 680 681 CONECT 679 678 CONECT 680 678 -CONECT 681 678 682 691 -CONECT 682 681 683 684 +CONECT 681 678 682 682 691 +CONECT 682 681 681 683 684 CONECT 683 682 -CONECT 684 682 685 686 +CONECT 684 682 685 686 686 CONECT 685 684 -CONECT 686 684 687 689 +CONECT 686 684 684 687 689 CONECT 687 686 688 CONECT 688 687 -CONECT 689 686 690 691 +CONECT 689 686 690 691 691 CONECT 690 689 -CONECT 691 681 689 692 +CONECT 691 681 689 689 692 CONECT 692 691 -CONECT 693 676 694 695 -CONECT 694 693 +CONECT 693 676 694 694 695 +CONECT 694 693 693 CONECT 695 693 696 697 CONECT 696 695 CONECT 697 695 698 699 705 @@ -1559,11 +1559,11 @@ CONECT 698 697 CONECT 699 697 700 701 702 CONECT 700 699 CONECT 701 699 -CONECT 702 699 703 704 -CONECT 703 702 +CONECT 702 699 703 703 704 +CONECT 703 702 702 CONECT 704 702 -CONECT 705 697 706 707 -CONECT 706 705 +CONECT 705 697 706 706 707 +CONECT 706 705 705 CONECT 707 705 708 709 CONECT 708 707 CONECT 709 707 710 711 717 @@ -1571,11 +1571,11 @@ CONECT 710 709 CONECT 711 709 712 713 714 CONECT 712 711 CONECT 713 711 -CONECT 714 711 715 716 -CONECT 715 714 +CONECT 714 711 715 715 716 +CONECT 715 714 714 CONECT 716 714 -CONECT 717 709 718 719 -CONECT 718 717 +CONECT 717 709 718 718 719 +CONECT 718 717 717 CONECT 719 717 720 721 CONECT 720 719 CONECT 721 719 722 723 727 @@ -1584,8 +1584,8 @@ CONECT 723 721 724 725 726 CONECT 724 723 CONECT 725 723 CONECT 726 723 -CONECT 727 721 728 729 -CONECT 728 727 +CONECT 727 721 728 728 729 +CONECT 728 727 727 CONECT 729 727 730 731 CONECT 730 729 CONECT 731 729 732 733 741 @@ -1598,8 +1598,8 @@ CONECT 737 735 CONECT 738 735 CONECT 739 733 740 CONECT 740 739 -CONECT 741 731 742 743 -CONECT 742 741 +CONECT 741 731 742 742 743 +CONECT 742 741 741 CONECT 743 741 744 745 CONECT 744 743 CONECT 745 743 746 747 763 @@ -1620,8 +1620,8 @@ CONECT 759 756 760 761 762 CONECT 760 759 CONECT 761 759 CONECT 762 759 -CONECT 763 745 764 765 -CONECT 764 763 +CONECT 763 745 764 764 765 +CONECT 764 763 763 CONECT 765 763 766 767 CONECT 766 765 CONECT 767 765 768 769 777 @@ -1634,8 +1634,8 @@ CONECT 773 771 CONECT 774 771 CONECT 775 769 776 CONECT 776 775 -CONECT 777 767 778 779 -CONECT 778 777 +CONECT 777 767 778 778 779 +CONECT 778 777 777 CONECT 779 777 780 781 CONECT 780 779 CONECT 781 779 782 783 797 @@ -1643,19 +1643,19 @@ CONECT 782 781 CONECT 783 781 784 785 786 CONECT 784 783 CONECT 785 783 -CONECT 786 783 787 795 -CONECT 787 786 788 789 +CONECT 786 783 787 787 795 +CONECT 787 786 786 788 789 CONECT 788 787 -CONECT 789 787 790 791 +CONECT 789 787 790 791 791 CONECT 790 789 -CONECT 791 789 792 793 +CONECT 791 789 789 792 793 CONECT 792 791 -CONECT 793 791 794 795 +CONECT 793 791 794 795 795 CONECT 794 793 -CONECT 795 786 793 796 +CONECT 795 786 793 793 796 CONECT 796 795 -CONECT 797 781 798 799 -CONECT 798 797 +CONECT 797 781 798 798 799 +CONECT 798 797 797 CONECT 799 797 800 801 CONECT 800 799 CONECT 801 799 802 803 811 @@ -1668,8 +1668,8 @@ CONECT 807 805 CONECT 808 805 CONECT 809 803 810 CONECT 810 809 -CONECT 811 801 812 813 -CONECT 812 811 +CONECT 811 801 812 812 813 +CONECT 812 811 811 CONECT 813 811 814 815 CONECT 814 813 CONECT 815 813 816 817 827 @@ -1684,8 +1684,8 @@ CONECT 823 817 824 825 826 CONECT 824 823 CONECT 825 823 CONECT 826 823 -CONECT 827 815 828 829 -CONECT 828 827 +CONECT 827 815 828 828 829 +CONECT 828 827 827 CONECT 829 827 830 831 CONECT 830 829 CONECT 831 829 832 833 841 @@ -1698,8 +1698,8 @@ CONECT 837 835 CONECT 838 835 CONECT 839 833 840 CONECT 840 839 -CONECT 841 831 842 843 -CONECT 842 841 +CONECT 841 831 842 842 843 +CONECT 842 841 841 CONECT 843 841 844 845 CONECT 844 843 CONECT 845 843 846 847 856 @@ -1710,11 +1710,11 @@ CONECT 849 847 CONECT 850 847 851 852 853 CONECT 851 850 CONECT 852 850 -CONECT 853 850 854 855 -CONECT 854 853 +CONECT 853 850 854 854 855 +CONECT 854 853 853 CONECT 855 853 -CONECT 856 845 857 858 -CONECT 857 856 +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 index 80932d7..23c4be5 100644 --- a/unittests/output_files/test_thr_to_gly_restypeFalse.pdb +++ b/unittests/output_files/test_thr_to_gly_restypeFalse.pdb @@ -1,5 +1,5 @@ COMPND MET -AUTHOR GENERATED BY OPEN BABEL 2.4.1 +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 @@ -242,8 +242,8 @@ 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 O -ATOM 244 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O +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 @@ -299,8 +299,8 @@ 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 O -ATOM 301 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O +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 @@ -337,8 +337,8 @@ 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 O -ATOM 339 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O +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 @@ -396,8 +396,8 @@ 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 O -ATOM 398 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O +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 @@ -550,8 +550,8 @@ 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 O -ATOM 552 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O +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 @@ -599,8 +599,8 @@ 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 O -ATOM 601 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O +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 @@ -621,8 +621,8 @@ 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 O -ATOM 623 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O +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 @@ -692,8 +692,8 @@ 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 O -ATOM 694 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O +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 @@ -704,8 +704,8 @@ 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 O -ATOM 706 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O +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 @@ -843,11 +843,11 @@ 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 O -ATOM 845 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O +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 O -ATOM 848 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O +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 @@ -865,15 +865,15 @@ CONECT 14 13 15 16 17 CONECT 15 14 CONECT 16 14 CONECT 17 14 -CONECT 18 5 19 20 -CONECT 19 18 +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 27 -CONECT 26 25 +CONECT 25 22 26 26 27 +CONECT 26 25 25 CONECT 27 25 28 29 CONECT 28 27 CONECT 29 27 30 31 46 @@ -881,20 +881,20 @@ CONECT 30 29 CONECT 31 29 32 33 34 CONECT 32 31 CONECT 33 31 -CONECT 34 31 35 44 -CONECT 35 34 36 37 +CONECT 34 31 35 35 44 +CONECT 35 34 34 36 37 CONECT 36 35 -CONECT 37 35 38 39 +CONECT 37 35 38 39 39 CONECT 38 37 -CONECT 39 37 40 42 +CONECT 39 37 37 40 42 CONECT 40 39 41 CONECT 41 40 -CONECT 42 39 43 44 +CONECT 42 39 43 44 44 CONECT 43 42 -CONECT 44 34 42 45 +CONECT 44 34 42 42 45 CONECT 45 44 -CONECT 46 29 47 48 -CONECT 47 46 +CONECT 46 29 47 47 48 +CONECT 47 46 46 CONECT 48 46 49 50 CONECT 49 48 CONECT 50 48 51 52 68 @@ -915,8 +915,8 @@ CONECT 64 61 65 66 67 CONECT 65 64 CONECT 66 64 CONECT 67 64 -CONECT 68 50 69 70 -CONECT 69 68 +CONECT 68 50 69 69 70 +CONECT 69 68 68 CONECT 70 68 71 72 CONECT 71 70 CONECT 72 70 73 74 87 @@ -934,8 +934,8 @@ CONECT 83 77 84 85 86 CONECT 84 83 CONECT 85 83 CONECT 86 83 -CONECT 87 72 88 89 -CONECT 88 87 +CONECT 87 72 88 88 89 +CONECT 88 87 87 CONECT 89 87 90 91 CONECT 90 89 CONECT 91 89 92 93 106 @@ -953,8 +953,8 @@ CONECT 102 99 103 104 105 CONECT 103 102 CONECT 104 102 CONECT 105 102 -CONECT 106 91 107 108 -CONECT 107 106 +CONECT 106 91 107 107 108 +CONECT 107 106 106 CONECT 108 106 109 110 CONECT 109 108 CONECT 110 108 111 112 125 @@ -972,8 +972,8 @@ CONECT 121 115 122 123 124 CONECT 122 121 CONECT 123 121 CONECT 124 121 -CONECT 125 110 126 127 -CONECT 126 125 +CONECT 125 110 126 126 127 +CONECT 126 125 125 CONECT 127 125 128 129 CONECT 128 127 CONECT 129 127 130 131 139 @@ -981,20 +981,20 @@ CONECT 130 129 CONECT 131 129 132 133 134 CONECT 132 131 CONECT 133 131 -CONECT 134 131 135 136 -CONECT 135 134 +CONECT 134 131 135 135 136 +CONECT 135 134 134 CONECT 136 134 137 138 CONECT 137 136 CONECT 138 136 -CONECT 139 129 140 141 -CONECT 140 139 +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 146 143 147 148 -CONECT 147 146 +CONECT 146 143 147 147 148 +CONECT 147 146 146 CONECT 148 146 149 150 CONECT 149 148 CONECT 150 148 151 152 168 @@ -1015,8 +1015,8 @@ CONECT 164 161 165 166 167 CONECT 165 164 CONECT 166 164 CONECT 167 164 -CONECT 168 150 169 170 -CONECT 169 168 +CONECT 168 150 169 169 170 +CONECT 169 168 168 CONECT 170 168 171 172 CONECT 171 170 CONECT 172 170 173 174 182 @@ -1029,8 +1029,8 @@ CONECT 178 176 CONECT 179 176 CONECT 180 174 181 CONECT 181 180 -CONECT 182 172 183 184 -CONECT 183 182 +CONECT 182 172 183 183 184 +CONECT 183 182 182 CONECT 184 182 185 186 CONECT 185 184 CONECT 186 184 187 188 201 @@ -1048,8 +1048,8 @@ CONECT 197 191 198 199 200 CONECT 198 197 CONECT 199 197 CONECT 200 197 -CONECT 201 186 202 203 -CONECT 202 201 +CONECT 201 186 202 202 203 +CONECT 202 201 201 CONECT 203 201 204 205 CONECT 204 203 CONECT 205 203 206 207 223 @@ -1070,15 +1070,15 @@ CONECT 219 216 220 221 222 CONECT 220 219 CONECT 221 219 CONECT 222 219 -CONECT 223 205 224 225 -CONECT 224 223 +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 230 227 231 232 -CONECT 231 230 +CONECT 230 227 231 231 232 +CONECT 231 230 230 CONECT 232 230 233 234 CONECT 233 232 CONECT 234 232 235 236 245 @@ -1089,11 +1089,11 @@ CONECT 238 236 CONECT 239 236 240 241 242 CONECT 240 239 CONECT 241 239 -CONECT 242 239 243 244 -CONECT 243 242 +CONECT 242 239 243 243 244 +CONECT 243 242 242 CONECT 244 242 -CONECT 245 234 246 247 -CONECT 246 245 +CONECT 245 234 246 246 247 +CONECT 246 245 245 CONECT 247 245 248 249 CONECT 248 247 CONECT 249 247 250 251 259 @@ -1106,8 +1106,8 @@ CONECT 255 253 CONECT 256 253 CONECT 257 251 258 CONECT 258 257 -CONECT 259 249 260 261 -CONECT 260 259 +CONECT 259 249 260 260 261 +CONECT 260 259 259 CONECT 261 259 262 263 CONECT 262 261 CONECT 263 261 264 265 273 @@ -1120,8 +1120,8 @@ CONECT 269 267 CONECT 270 267 CONECT 271 265 272 CONECT 272 271 -CONECT 273 263 274 275 -CONECT 274 273 +CONECT 273 263 274 274 275 +CONECT 274 273 273 CONECT 275 273 276 277 CONECT 276 275 CONECT 277 275 278 279 287 @@ -1134,8 +1134,8 @@ CONECT 283 281 CONECT 284 281 CONECT 285 279 286 CONECT 286 285 -CONECT 287 277 288 289 -CONECT 288 287 +CONECT 287 277 288 288 289 +CONECT 288 287 287 CONECT 289 287 290 291 CONECT 290 289 CONECT 291 289 292 293 302 @@ -1146,11 +1146,11 @@ CONECT 295 293 CONECT 296 293 297 298 299 CONECT 297 296 CONECT 298 296 -CONECT 299 296 300 301 -CONECT 300 299 +CONECT 299 296 300 300 301 +CONECT 300 299 299 CONECT 301 299 -CONECT 302 291 303 304 -CONECT 303 302 +CONECT 302 291 303 303 304 +CONECT 303 302 302 CONECT 304 302 305 306 CONECT 305 304 CONECT 306 304 307 308 312 @@ -1159,8 +1159,8 @@ CONECT 308 306 309 310 311 CONECT 309 308 CONECT 310 308 CONECT 311 308 -CONECT 312 306 313 314 -CONECT 313 312 +CONECT 312 306 313 313 314 +CONECT 313 312 312 CONECT 314 312 315 316 CONECT 315 314 CONECT 316 314 317 318 328 @@ -1175,8 +1175,8 @@ CONECT 324 318 325 326 327 CONECT 325 324 CONECT 326 324 CONECT 327 324 -CONECT 328 316 329 330 -CONECT 329 328 +CONECT 328 316 329 329 330 +CONECT 329 328 328 CONECT 330 328 331 332 CONECT 331 330 CONECT 332 330 333 334 340 @@ -1184,11 +1184,11 @@ CONECT 333 332 CONECT 334 332 335 336 337 CONECT 335 334 CONECT 336 334 -CONECT 337 334 338 339 -CONECT 338 337 +CONECT 337 334 338 338 339 +CONECT 338 337 337 CONECT 339 337 -CONECT 340 332 341 342 -CONECT 341 340 +CONECT 340 332 341 341 342 +CONECT 341 340 340 CONECT 342 340 343 344 CONECT 343 342 CONECT 344 342 345 346 350 @@ -1197,8 +1197,8 @@ CONECT 346 344 347 348 349 CONECT 347 346 CONECT 348 346 CONECT 349 346 -CONECT 350 344 351 352 -CONECT 351 350 +CONECT 350 344 351 351 352 +CONECT 351 350 350 CONECT 352 350 353 354 CONECT 353 352 CONECT 354 352 355 356 360 @@ -1207,8 +1207,8 @@ CONECT 356 354 357 358 359 CONECT 357 356 CONECT 358 356 CONECT 359 356 -CONECT 360 354 361 362 -CONECT 361 360 +CONECT 360 354 361 361 362 +CONECT 361 360 360 CONECT 362 360 363 364 CONECT 363 362 CONECT 364 362 365 366 374 @@ -1221,8 +1221,8 @@ CONECT 370 368 CONECT 371 368 CONECT 372 366 373 CONECT 373 372 -CONECT 374 364 375 376 -CONECT 375 374 +CONECT 374 364 375 375 376 +CONECT 375 374 374 CONECT 376 374 377 378 CONECT 377 376 CONECT 378 376 379 380 384 @@ -1231,8 +1231,8 @@ CONECT 380 378 381 382 383 CONECT 381 380 CONECT 382 380 CONECT 383 380 -CONECT 384 378 385 386 -CONECT 385 384 +CONECT 384 378 385 385 386 +CONECT 385 384 384 CONECT 386 384 387 388 CONECT 387 386 CONECT 388 386 389 390 399 @@ -1243,11 +1243,11 @@ CONECT 392 390 CONECT 393 390 394 395 396 CONECT 394 393 CONECT 395 393 -CONECT 396 393 397 398 -CONECT 397 396 +CONECT 396 393 397 397 398 +CONECT 397 396 396 CONECT 398 396 -CONECT 399 388 400 401 -CONECT 400 399 +CONECT 399 388 400 400 401 +CONECT 400 399 399 CONECT 401 399 402 403 CONECT 402 401 CONECT 403 401 404 405 421 @@ -1268,8 +1268,8 @@ CONECT 417 414 418 419 420 CONECT 418 417 CONECT 419 417 CONECT 420 417 -CONECT 421 403 422 423 -CONECT 422 421 +CONECT 421 403 422 422 423 +CONECT 422 421 421 CONECT 423 421 424 425 CONECT 424 423 CONECT 425 423 426 427 437 @@ -1284,8 +1284,8 @@ CONECT 433 427 434 435 436 CONECT 434 433 CONECT 435 433 CONECT 436 433 -CONECT 437 425 438 439 -CONECT 438 437 +CONECT 437 425 438 438 439 +CONECT 438 437 437 CONECT 439 437 440 441 CONECT 440 439 CONECT 441 439 442 443 457 @@ -1293,19 +1293,19 @@ CONECT 442 441 CONECT 443 441 444 445 446 CONECT 444 443 CONECT 445 443 -CONECT 446 443 447 455 -CONECT 447 446 448 449 +CONECT 446 443 447 447 455 +CONECT 447 446 446 448 449 CONECT 448 447 -CONECT 449 447 450 451 +CONECT 449 447 450 451 451 CONECT 450 449 -CONECT 451 449 452 453 +CONECT 451 449 449 452 453 CONECT 452 451 -CONECT 453 451 454 455 +CONECT 453 451 454 455 455 CONECT 454 453 -CONECT 455 446 453 456 +CONECT 455 446 453 453 456 CONECT 456 455 -CONECT 457 441 458 459 -CONECT 458 457 +CONECT 457 441 458 458 459 +CONECT 458 457 457 CONECT 459 457 460 461 CONECT 460 459 CONECT 461 459 462 463 479 @@ -1326,8 +1326,8 @@ CONECT 475 472 476 477 478 CONECT 476 475 CONECT 477 475 CONECT 478 475 -CONECT 479 461 480 481 -CONECT 480 479 +CONECT 479 461 480 480 481 +CONECT 480 479 479 CONECT 481 479 482 483 CONECT 482 481 CONECT 483 481 484 485 496 @@ -1338,13 +1338,13 @@ CONECT 487 485 CONECT 488 485 489 490 491 CONECT 489 488 CONECT 490 488 -CONECT 491 488 492 493 -CONECT 492 491 +CONECT 491 488 492 492 493 +CONECT 492 491 491 CONECT 493 491 494 495 CONECT 494 493 CONECT 495 493 -CONECT 496 483 497 498 -CONECT 497 496 +CONECT 496 483 497 497 498 +CONECT 497 496 496 CONECT 498 496 499 500 CONECT 499 498 CONECT 500 498 501 502 517 @@ -1352,20 +1352,20 @@ CONECT 501 500 CONECT 502 500 503 504 505 CONECT 503 502 CONECT 504 502 -CONECT 505 502 506 515 -CONECT 506 505 507 508 +CONECT 505 502 506 506 515 +CONECT 506 505 505 507 508 CONECT 507 506 -CONECT 508 506 509 510 +CONECT 508 506 509 510 510 CONECT 509 508 -CONECT 510 508 511 513 +CONECT 510 508 508 511 513 CONECT 511 510 512 CONECT 512 511 -CONECT 513 510 514 515 +CONECT 513 510 514 515 515 CONECT 514 513 -CONECT 515 505 513 516 +CONECT 515 505 513 513 516 CONECT 516 515 -CONECT 517 500 518 519 -CONECT 518 517 +CONECT 517 500 518 518 519 +CONECT 518 517 517 CONECT 519 517 520 521 CONECT 520 519 CONECT 521 519 522 523 527 @@ -1374,8 +1374,8 @@ CONECT 523 521 524 525 526 CONECT 524 523 CONECT 525 523 CONECT 526 523 -CONECT 527 521 528 529 -CONECT 528 527 +CONECT 527 521 528 528 529 +CONECT 528 527 527 CONECT 529 527 530 531 CONECT 530 529 CONECT 531 529 532 533 541 @@ -1383,13 +1383,13 @@ CONECT 532 531 CONECT 533 531 534 535 536 CONECT 534 533 CONECT 535 533 -CONECT 536 533 537 538 -CONECT 537 536 +CONECT 536 533 537 537 538 +CONECT 537 536 536 CONECT 538 536 539 540 CONECT 539 538 CONECT 540 538 -CONECT 541 531 542 543 -CONECT 542 541 +CONECT 541 531 542 542 543 +CONECT 542 541 541 CONECT 543 541 544 545 CONECT 544 543 CONECT 545 543 546 547 553 @@ -1397,11 +1397,11 @@ CONECT 546 545 CONECT 547 545 548 549 550 CONECT 548 547 CONECT 549 547 -CONECT 550 547 551 552 -CONECT 551 550 +CONECT 550 547 551 551 552 +CONECT 551 550 550 CONECT 552 550 -CONECT 553 545 554 555 -CONECT 554 553 +CONECT 553 545 554 554 555 +CONECT 554 553 553 CONECT 555 553 556 557 CONECT 556 555 CONECT 557 555 558 559 567 @@ -1409,20 +1409,20 @@ CONECT 558 557 CONECT 559 557 560 561 562 CONECT 560 559 CONECT 561 559 -CONECT 562 559 563 564 -CONECT 563 562 +CONECT 562 559 563 563 564 +CONECT 563 562 562 CONECT 564 562 565 566 CONECT 565 564 CONECT 566 564 -CONECT 567 557 568 569 -CONECT 568 567 +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 574 571 575 576 -CONECT 575 574 +CONECT 574 571 575 575 576 +CONECT 575 574 574 CONECT 576 574 577 578 CONECT 577 576 CONECT 578 576 579 580 590 @@ -1437,8 +1437,8 @@ CONECT 586 580 587 588 589 CONECT 587 586 CONECT 588 586 CONECT 589 586 -CONECT 590 578 591 592 -CONECT 591 590 +CONECT 590 578 591 591 592 +CONECT 591 590 590 CONECT 592 590 593 594 CONECT 593 592 CONECT 594 592 595 596 602 @@ -1446,18 +1446,18 @@ CONECT 595 594 CONECT 596 594 597 598 599 CONECT 597 596 CONECT 598 596 -CONECT 599 596 600 601 -CONECT 600 599 +CONECT 599 596 600 600 601 +CONECT 600 599 599 CONECT 601 599 -CONECT 602 594 603 604 -CONECT 603 602 +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 609 606 610 611 -CONECT 610 609 +CONECT 609 606 610 610 611 +CONECT 610 609 609 CONECT 611 609 612 613 CONECT 612 611 CONECT 613 611 614 615 624 @@ -1468,11 +1468,11 @@ CONECT 617 615 CONECT 618 615 619 620 621 CONECT 619 618 CONECT 620 618 -CONECT 621 618 622 623 -CONECT 622 621 +CONECT 621 618 622 622 623 +CONECT 622 621 621 CONECT 623 621 -CONECT 624 613 625 626 -CONECT 625 624 +CONECT 624 613 625 625 626 +CONECT 625 624 624 CONECT 626 624 627 628 CONECT 627 626 CONECT 628 626 629 630 648 @@ -1480,23 +1480,23 @@ CONECT 629 628 CONECT 630 628 631 632 633 CONECT 631 630 CONECT 632 630 -CONECT 633 630 634 647 -CONECT 634 633 635 636 +CONECT 633 630 634 634 647 +CONECT 634 633 633 635 636 CONECT 635 634 CONECT 636 634 637 638 CONECT 637 636 -CONECT 638 636 639 647 -CONECT 639 638 640 641 +CONECT 638 636 639 639 647 +CONECT 639 638 638 640 641 CONECT 640 639 -CONECT 641 639 642 643 +CONECT 641 639 642 643 643 CONECT 642 641 -CONECT 643 641 644 645 +CONECT 643 641 641 644 645 CONECT 644 643 -CONECT 645 643 646 647 +CONECT 645 643 646 647 647 CONECT 646 645 -CONECT 647 633 638 645 -CONECT 648 628 649 650 -CONECT 649 648 +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 @@ -1509,8 +1509,8 @@ CONECT 658 656 CONECT 659 656 CONECT 660 654 661 CONECT 661 660 -CONECT 662 652 663 664 -CONECT 663 662 +CONECT 662 652 663 663 664 +CONECT 663 662 662 CONECT 664 662 665 666 CONECT 665 664 CONECT 666 664 667 668 683 @@ -1518,20 +1518,20 @@ CONECT 667 666 CONECT 668 666 669 670 671 CONECT 669 668 CONECT 670 668 -CONECT 671 668 672 681 -CONECT 672 671 673 674 +CONECT 671 668 672 672 681 +CONECT 672 671 671 673 674 CONECT 673 672 -CONECT 674 672 675 676 +CONECT 674 672 675 676 676 CONECT 675 674 -CONECT 676 674 677 679 +CONECT 676 674 674 677 679 CONECT 677 676 678 CONECT 678 677 -CONECT 679 676 680 681 +CONECT 679 676 680 681 681 CONECT 680 679 -CONECT 681 671 679 682 +CONECT 681 671 679 679 682 CONECT 682 681 -CONECT 683 666 684 685 -CONECT 684 683 +CONECT 683 666 684 684 685 +CONECT 684 683 683 CONECT 685 683 686 687 CONECT 686 685 CONECT 687 685 688 689 695 @@ -1539,11 +1539,11 @@ CONECT 688 687 CONECT 689 687 690 691 692 CONECT 690 689 CONECT 691 689 -CONECT 692 689 693 694 -CONECT 693 692 +CONECT 692 689 693 693 694 +CONECT 693 692 692 CONECT 694 692 -CONECT 695 687 696 697 -CONECT 696 695 +CONECT 695 687 696 696 697 +CONECT 696 695 695 CONECT 697 695 698 699 CONECT 698 697 CONECT 699 697 700 701 707 @@ -1551,11 +1551,11 @@ CONECT 700 699 CONECT 701 699 702 703 704 CONECT 702 701 CONECT 703 701 -CONECT 704 701 705 706 -CONECT 705 704 +CONECT 704 701 705 705 706 +CONECT 705 704 704 CONECT 706 704 -CONECT 707 699 708 709 -CONECT 708 707 +CONECT 707 699 708 708 709 +CONECT 708 707 707 CONECT 709 707 710 711 CONECT 710 709 CONECT 711 709 712 713 717 @@ -1564,8 +1564,8 @@ CONECT 713 711 714 715 716 CONECT 714 713 CONECT 715 713 CONECT 716 713 -CONECT 717 711 718 719 -CONECT 718 717 +CONECT 717 711 718 718 719 +CONECT 718 717 717 CONECT 719 717 720 721 CONECT 720 719 CONECT 721 719 722 723 731 @@ -1578,8 +1578,8 @@ CONECT 727 725 CONECT 728 725 CONECT 729 723 730 CONECT 730 729 -CONECT 731 721 732 733 -CONECT 732 731 +CONECT 731 721 732 732 733 +CONECT 732 731 731 CONECT 733 731 734 735 CONECT 734 733 CONECT 735 733 736 737 753 @@ -1600,8 +1600,8 @@ CONECT 749 746 750 751 752 CONECT 750 749 CONECT 751 749 CONECT 752 749 -CONECT 753 735 754 755 -CONECT 754 753 +CONECT 753 735 754 754 755 +CONECT 754 753 753 CONECT 755 753 756 757 CONECT 756 755 CONECT 757 755 758 759 767 @@ -1614,8 +1614,8 @@ CONECT 763 761 CONECT 764 761 CONECT 765 759 766 CONECT 766 765 -CONECT 767 757 768 769 -CONECT 768 767 +CONECT 767 757 768 768 769 +CONECT 768 767 767 CONECT 769 767 770 771 CONECT 770 769 CONECT 771 769 772 773 787 @@ -1623,19 +1623,19 @@ CONECT 772 771 CONECT 773 771 774 775 776 CONECT 774 773 CONECT 775 773 -CONECT 776 773 777 785 -CONECT 777 776 778 779 +CONECT 776 773 777 777 785 +CONECT 777 776 776 778 779 CONECT 778 777 -CONECT 779 777 780 781 +CONECT 779 777 780 781 781 CONECT 780 779 -CONECT 781 779 782 783 +CONECT 781 779 779 782 783 CONECT 782 781 -CONECT 783 781 784 785 +CONECT 783 781 784 785 785 CONECT 784 783 -CONECT 785 776 783 786 +CONECT 785 776 783 783 786 CONECT 786 785 -CONECT 787 771 788 789 -CONECT 788 787 +CONECT 787 771 788 788 789 +CONECT 788 787 787 CONECT 789 787 790 791 CONECT 790 789 CONECT 791 789 792 793 801 @@ -1648,8 +1648,8 @@ CONECT 797 795 CONECT 798 795 CONECT 799 793 800 CONECT 800 799 -CONECT 801 791 802 803 -CONECT 802 801 +CONECT 801 791 802 802 803 +CONECT 802 801 801 CONECT 803 801 804 805 CONECT 804 803 CONECT 805 803 806 807 817 @@ -1664,8 +1664,8 @@ CONECT 813 807 814 815 816 CONECT 814 813 CONECT 815 813 CONECT 816 813 -CONECT 817 805 818 819 -CONECT 818 817 +CONECT 817 805 818 818 819 +CONECT 818 817 817 CONECT 819 817 820 821 CONECT 820 819 CONECT 821 819 822 823 831 @@ -1678,8 +1678,8 @@ CONECT 827 825 CONECT 828 825 CONECT 829 823 830 CONECT 830 829 -CONECT 831 821 832 833 -CONECT 832 831 +CONECT 831 821 832 832 833 +CONECT 832 831 831 CONECT 833 831 834 835 CONECT 834 833 CONECT 835 833 836 837 846 @@ -1690,11 +1690,11 @@ CONECT 839 837 CONECT 840 837 841 842 843 CONECT 841 840 CONECT 842 840 -CONECT 843 840 844 845 -CONECT 844 843 +CONECT 843 840 844 844 845 +CONECT 844 843 843 CONECT 845 843 -CONECT 846 835 847 848 -CONECT 847 846 +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 index 64e72b7..5370589 100644 --- a/unittests/output_files/test_thr_to_gly_restypeTrue.pdb +++ b/unittests/output_files/test_thr_to_gly_restypeTrue.pdb @@ -1,5 +1,5 @@ COMPND MET -AUTHOR GENERATED BY OPEN BABEL 2.4.1 +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 @@ -242,8 +242,8 @@ 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 O -ATOM 244 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O +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 @@ -299,8 +299,8 @@ 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 O -ATOM 301 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O +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 @@ -337,8 +337,8 @@ 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 O -ATOM 339 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O +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 @@ -396,8 +396,8 @@ 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 O -ATOM 398 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O +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 @@ -550,8 +550,8 @@ 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 O -ATOM 552 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O +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 @@ -599,8 +599,8 @@ 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 O -ATOM 601 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O +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 @@ -621,8 +621,8 @@ 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 O -ATOM 623 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O +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 @@ -692,8 +692,8 @@ 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 O -ATOM 694 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O +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 @@ -704,8 +704,8 @@ 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 O -ATOM 706 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O +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 @@ -843,11 +843,11 @@ 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 O -ATOM 845 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O +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 O -ATOM 848 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O +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 @@ -865,15 +865,15 @@ CONECT 14 13 15 16 17 CONECT 15 14 CONECT 16 14 CONECT 17 14 -CONECT 18 5 19 20 -CONECT 19 18 +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 27 -CONECT 26 25 +CONECT 25 22 26 26 27 +CONECT 26 25 25 CONECT 27 25 28 29 CONECT 28 27 CONECT 29 27 30 31 46 @@ -881,20 +881,20 @@ CONECT 30 29 CONECT 31 29 32 33 34 CONECT 32 31 CONECT 33 31 -CONECT 34 31 35 44 -CONECT 35 34 36 37 +CONECT 34 31 35 35 44 +CONECT 35 34 34 36 37 CONECT 36 35 -CONECT 37 35 38 39 +CONECT 37 35 38 39 39 CONECT 38 37 -CONECT 39 37 40 42 +CONECT 39 37 37 40 42 CONECT 40 39 41 CONECT 41 40 -CONECT 42 39 43 44 +CONECT 42 39 43 44 44 CONECT 43 42 -CONECT 44 34 42 45 +CONECT 44 34 42 42 45 CONECT 45 44 -CONECT 46 29 47 48 -CONECT 47 46 +CONECT 46 29 47 47 48 +CONECT 47 46 46 CONECT 48 46 49 50 CONECT 49 48 CONECT 50 48 51 52 68 @@ -915,8 +915,8 @@ CONECT 64 61 65 66 67 CONECT 65 64 CONECT 66 64 CONECT 67 64 -CONECT 68 50 69 70 -CONECT 69 68 +CONECT 68 50 69 69 70 +CONECT 69 68 68 CONECT 70 68 71 72 CONECT 71 70 CONECT 72 70 73 74 87 @@ -934,8 +934,8 @@ CONECT 83 77 84 85 86 CONECT 84 83 CONECT 85 83 CONECT 86 83 -CONECT 87 72 88 89 -CONECT 88 87 +CONECT 87 72 88 88 89 +CONECT 88 87 87 CONECT 89 87 90 91 CONECT 90 89 CONECT 91 89 92 93 106 @@ -953,8 +953,8 @@ CONECT 102 99 103 104 105 CONECT 103 102 CONECT 104 102 CONECT 105 102 -CONECT 106 91 107 108 -CONECT 107 106 +CONECT 106 91 107 107 108 +CONECT 107 106 106 CONECT 108 106 109 110 CONECT 109 108 CONECT 110 108 111 112 125 @@ -972,8 +972,8 @@ CONECT 121 115 122 123 124 CONECT 122 121 CONECT 123 121 CONECT 124 121 -CONECT 125 110 126 127 -CONECT 126 125 +CONECT 125 110 126 126 127 +CONECT 126 125 125 CONECT 127 125 128 129 CONECT 128 127 CONECT 129 127 130 131 139 @@ -981,20 +981,20 @@ CONECT 130 129 CONECT 131 129 132 133 134 CONECT 132 131 CONECT 133 131 -CONECT 134 131 135 136 -CONECT 135 134 +CONECT 134 131 135 135 136 +CONECT 135 134 134 CONECT 136 134 137 138 CONECT 137 136 CONECT 138 136 -CONECT 139 129 140 141 -CONECT 140 139 +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 146 143 147 148 -CONECT 147 146 +CONECT 146 143 147 147 148 +CONECT 147 146 146 CONECT 148 146 149 150 CONECT 149 148 CONECT 150 148 151 152 168 @@ -1015,8 +1015,8 @@ CONECT 164 161 165 166 167 CONECT 165 164 CONECT 166 164 CONECT 167 164 -CONECT 168 150 169 170 -CONECT 169 168 +CONECT 168 150 169 169 170 +CONECT 169 168 168 CONECT 170 168 171 172 CONECT 171 170 CONECT 172 170 173 174 182 @@ -1029,8 +1029,8 @@ CONECT 178 176 CONECT 179 176 CONECT 180 174 181 CONECT 181 180 -CONECT 182 172 183 184 -CONECT 183 182 +CONECT 182 172 183 183 184 +CONECT 183 182 182 CONECT 184 182 185 186 CONECT 185 184 CONECT 186 184 187 188 201 @@ -1048,8 +1048,8 @@ CONECT 197 191 198 199 200 CONECT 198 197 CONECT 199 197 CONECT 200 197 -CONECT 201 186 202 203 -CONECT 202 201 +CONECT 201 186 202 202 203 +CONECT 202 201 201 CONECT 203 201 204 205 CONECT 204 203 CONECT 205 203 206 207 223 @@ -1070,15 +1070,15 @@ CONECT 219 216 220 221 222 CONECT 220 219 CONECT 221 219 CONECT 222 219 -CONECT 223 205 224 225 -CONECT 224 223 +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 230 227 231 232 -CONECT 231 230 +CONECT 230 227 231 231 232 +CONECT 231 230 230 CONECT 232 230 233 234 CONECT 233 232 CONECT 234 232 235 236 245 @@ -1089,11 +1089,11 @@ CONECT 238 236 CONECT 239 236 240 241 242 CONECT 240 239 CONECT 241 239 -CONECT 242 239 243 244 -CONECT 243 242 +CONECT 242 239 243 243 244 +CONECT 243 242 242 CONECT 244 242 -CONECT 245 234 246 247 -CONECT 246 245 +CONECT 245 234 246 246 247 +CONECT 246 245 245 CONECT 247 245 248 249 CONECT 248 247 CONECT 249 247 250 251 259 @@ -1106,8 +1106,8 @@ CONECT 255 253 CONECT 256 253 CONECT 257 251 258 CONECT 258 257 -CONECT 259 249 260 261 -CONECT 260 259 +CONECT 259 249 260 260 261 +CONECT 260 259 259 CONECT 261 259 262 263 CONECT 262 261 CONECT 263 261 264 265 273 @@ -1120,8 +1120,8 @@ CONECT 269 267 CONECT 270 267 CONECT 271 265 272 CONECT 272 271 -CONECT 273 263 274 275 -CONECT 274 273 +CONECT 273 263 274 274 275 +CONECT 274 273 273 CONECT 275 273 276 277 CONECT 276 275 CONECT 277 275 278 279 287 @@ -1134,8 +1134,8 @@ CONECT 283 281 CONECT 284 281 CONECT 285 279 286 CONECT 286 285 -CONECT 287 277 288 289 -CONECT 288 287 +CONECT 287 277 288 288 289 +CONECT 288 287 287 CONECT 289 287 290 291 CONECT 290 289 CONECT 291 289 292 293 302 @@ -1146,11 +1146,11 @@ CONECT 295 293 CONECT 296 293 297 298 299 CONECT 297 296 CONECT 298 296 -CONECT 299 296 300 301 -CONECT 300 299 +CONECT 299 296 300 300 301 +CONECT 300 299 299 CONECT 301 299 -CONECT 302 291 303 304 -CONECT 303 302 +CONECT 302 291 303 303 304 +CONECT 303 302 302 CONECT 304 302 305 306 CONECT 305 304 CONECT 306 304 307 308 312 @@ -1159,8 +1159,8 @@ CONECT 308 306 309 310 311 CONECT 309 308 CONECT 310 308 CONECT 311 308 -CONECT 312 306 313 314 -CONECT 313 312 +CONECT 312 306 313 313 314 +CONECT 313 312 312 CONECT 314 312 315 316 CONECT 315 314 CONECT 316 314 317 318 328 @@ -1175,8 +1175,8 @@ CONECT 324 318 325 326 327 CONECT 325 324 CONECT 326 324 CONECT 327 324 -CONECT 328 316 329 330 -CONECT 329 328 +CONECT 328 316 329 329 330 +CONECT 329 328 328 CONECT 330 328 331 332 CONECT 331 330 CONECT 332 330 333 334 340 @@ -1184,11 +1184,11 @@ CONECT 333 332 CONECT 334 332 335 336 337 CONECT 335 334 CONECT 336 334 -CONECT 337 334 338 339 -CONECT 338 337 +CONECT 337 334 338 338 339 +CONECT 338 337 337 CONECT 339 337 -CONECT 340 332 341 342 -CONECT 341 340 +CONECT 340 332 341 341 342 +CONECT 341 340 340 CONECT 342 340 343 344 CONECT 343 342 CONECT 344 342 345 346 350 @@ -1197,8 +1197,8 @@ CONECT 346 344 347 348 349 CONECT 347 346 CONECT 348 346 CONECT 349 346 -CONECT 350 344 351 352 -CONECT 351 350 +CONECT 350 344 351 351 352 +CONECT 351 350 350 CONECT 352 350 353 354 CONECT 353 352 CONECT 354 352 355 356 360 @@ -1207,8 +1207,8 @@ CONECT 356 354 357 358 359 CONECT 357 356 CONECT 358 356 CONECT 359 356 -CONECT 360 354 361 362 -CONECT 361 360 +CONECT 360 354 361 361 362 +CONECT 361 360 360 CONECT 362 360 363 364 CONECT 363 362 CONECT 364 362 365 366 374 @@ -1221,8 +1221,8 @@ CONECT 370 368 CONECT 371 368 CONECT 372 366 373 CONECT 373 372 -CONECT 374 364 375 376 -CONECT 375 374 +CONECT 374 364 375 375 376 +CONECT 375 374 374 CONECT 376 374 377 378 CONECT 377 376 CONECT 378 376 379 380 384 @@ -1231,8 +1231,8 @@ CONECT 380 378 381 382 383 CONECT 381 380 CONECT 382 380 CONECT 383 380 -CONECT 384 378 385 386 -CONECT 385 384 +CONECT 384 378 385 385 386 +CONECT 385 384 384 CONECT 386 384 387 388 CONECT 387 386 CONECT 388 386 389 390 399 @@ -1243,11 +1243,11 @@ CONECT 392 390 CONECT 393 390 394 395 396 CONECT 394 393 CONECT 395 393 -CONECT 396 393 397 398 -CONECT 397 396 +CONECT 396 393 397 397 398 +CONECT 397 396 396 CONECT 398 396 -CONECT 399 388 400 401 -CONECT 400 399 +CONECT 399 388 400 400 401 +CONECT 400 399 399 CONECT 401 399 402 403 CONECT 402 401 CONECT 403 401 404 405 421 @@ -1268,8 +1268,8 @@ CONECT 417 414 418 419 420 CONECT 418 417 CONECT 419 417 CONECT 420 417 -CONECT 421 403 422 423 -CONECT 422 421 +CONECT 421 403 422 422 423 +CONECT 422 421 421 CONECT 423 421 424 425 CONECT 424 423 CONECT 425 423 426 427 437 @@ -1284,8 +1284,8 @@ CONECT 433 427 434 435 436 CONECT 434 433 CONECT 435 433 CONECT 436 433 -CONECT 437 425 438 439 -CONECT 438 437 +CONECT 437 425 438 438 439 +CONECT 438 437 437 CONECT 439 437 440 441 CONECT 440 439 CONECT 441 439 442 443 457 @@ -1293,19 +1293,19 @@ CONECT 442 441 CONECT 443 441 444 445 446 CONECT 444 443 CONECT 445 443 -CONECT 446 443 447 455 -CONECT 447 446 448 449 +CONECT 446 443 447 447 455 +CONECT 447 446 446 448 449 CONECT 448 447 -CONECT 449 447 450 451 +CONECT 449 447 450 451 451 CONECT 450 449 -CONECT 451 449 452 453 +CONECT 451 449 449 452 453 CONECT 452 451 -CONECT 453 451 454 455 +CONECT 453 451 454 455 455 CONECT 454 453 -CONECT 455 446 453 456 +CONECT 455 446 453 453 456 CONECT 456 455 -CONECT 457 441 458 459 -CONECT 458 457 +CONECT 457 441 458 458 459 +CONECT 458 457 457 CONECT 459 457 460 461 CONECT 460 459 CONECT 461 459 462 463 479 @@ -1326,8 +1326,8 @@ CONECT 475 472 476 477 478 CONECT 476 475 CONECT 477 475 CONECT 478 475 -CONECT 479 461 480 481 -CONECT 480 479 +CONECT 479 461 480 480 481 +CONECT 480 479 479 CONECT 481 479 482 483 CONECT 482 481 CONECT 483 481 484 485 496 @@ -1338,13 +1338,13 @@ CONECT 487 485 CONECT 488 485 489 490 491 CONECT 489 488 CONECT 490 488 -CONECT 491 488 492 493 -CONECT 492 491 +CONECT 491 488 492 492 493 +CONECT 492 491 491 CONECT 493 491 494 495 CONECT 494 493 CONECT 495 493 -CONECT 496 483 497 498 -CONECT 497 496 +CONECT 496 483 497 497 498 +CONECT 497 496 496 CONECT 498 496 499 500 CONECT 499 498 CONECT 500 498 501 502 517 @@ -1352,20 +1352,20 @@ CONECT 501 500 CONECT 502 500 503 504 505 CONECT 503 502 CONECT 504 502 -CONECT 505 502 506 515 -CONECT 506 505 507 508 +CONECT 505 502 506 506 515 +CONECT 506 505 505 507 508 CONECT 507 506 -CONECT 508 506 509 510 +CONECT 508 506 509 510 510 CONECT 509 508 -CONECT 510 508 511 513 +CONECT 510 508 508 511 513 CONECT 511 510 512 CONECT 512 511 -CONECT 513 510 514 515 +CONECT 513 510 514 515 515 CONECT 514 513 -CONECT 515 505 513 516 +CONECT 515 505 513 513 516 CONECT 516 515 -CONECT 517 500 518 519 -CONECT 518 517 +CONECT 517 500 518 518 519 +CONECT 518 517 517 CONECT 519 517 520 521 CONECT 520 519 CONECT 521 519 522 523 527 @@ -1374,8 +1374,8 @@ CONECT 523 521 524 525 526 CONECT 524 523 CONECT 525 523 CONECT 526 523 -CONECT 527 521 528 529 -CONECT 528 527 +CONECT 527 521 528 528 529 +CONECT 528 527 527 CONECT 529 527 530 531 CONECT 530 529 CONECT 531 529 532 533 541 @@ -1383,13 +1383,13 @@ CONECT 532 531 CONECT 533 531 534 535 536 CONECT 534 533 CONECT 535 533 -CONECT 536 533 537 538 -CONECT 537 536 +CONECT 536 533 537 537 538 +CONECT 537 536 536 CONECT 538 536 539 540 CONECT 539 538 CONECT 540 538 -CONECT 541 531 542 543 -CONECT 542 541 +CONECT 541 531 542 542 543 +CONECT 542 541 541 CONECT 543 541 544 545 CONECT 544 543 CONECT 545 543 546 547 553 @@ -1397,11 +1397,11 @@ CONECT 546 545 CONECT 547 545 548 549 550 CONECT 548 547 CONECT 549 547 -CONECT 550 547 551 552 -CONECT 551 550 +CONECT 550 547 551 551 552 +CONECT 551 550 550 CONECT 552 550 -CONECT 553 545 554 555 -CONECT 554 553 +CONECT 553 545 554 554 555 +CONECT 554 553 553 CONECT 555 553 556 557 CONECT 556 555 CONECT 557 555 558 559 567 @@ -1409,20 +1409,20 @@ CONECT 558 557 CONECT 559 557 560 561 562 CONECT 560 559 CONECT 561 559 -CONECT 562 559 563 564 -CONECT 563 562 +CONECT 562 559 563 563 564 +CONECT 563 562 562 CONECT 564 562 565 566 CONECT 565 564 CONECT 566 564 -CONECT 567 557 568 569 -CONECT 568 567 +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 574 571 575 576 -CONECT 575 574 +CONECT 574 571 575 575 576 +CONECT 575 574 574 CONECT 576 574 577 578 CONECT 577 576 CONECT 578 576 579 580 590 @@ -1437,8 +1437,8 @@ CONECT 586 580 587 588 589 CONECT 587 586 CONECT 588 586 CONECT 589 586 -CONECT 590 578 591 592 -CONECT 591 590 +CONECT 590 578 591 591 592 +CONECT 591 590 590 CONECT 592 590 593 594 CONECT 593 592 CONECT 594 592 595 596 602 @@ -1446,18 +1446,18 @@ CONECT 595 594 CONECT 596 594 597 598 599 CONECT 597 596 CONECT 598 596 -CONECT 599 596 600 601 -CONECT 600 599 +CONECT 599 596 600 600 601 +CONECT 600 599 599 CONECT 601 599 -CONECT 602 594 603 604 -CONECT 603 602 +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 609 606 610 611 -CONECT 610 609 +CONECT 609 606 610 610 611 +CONECT 610 609 609 CONECT 611 609 612 613 CONECT 612 611 CONECT 613 611 614 615 624 @@ -1468,11 +1468,11 @@ CONECT 617 615 CONECT 618 615 619 620 621 CONECT 619 618 CONECT 620 618 -CONECT 621 618 622 623 -CONECT 622 621 +CONECT 621 618 622 622 623 +CONECT 622 621 621 CONECT 623 621 -CONECT 624 613 625 626 -CONECT 625 624 +CONECT 624 613 625 625 626 +CONECT 625 624 624 CONECT 626 624 627 628 CONECT 627 626 CONECT 628 626 629 630 648 @@ -1480,23 +1480,23 @@ CONECT 629 628 CONECT 630 628 631 632 633 CONECT 631 630 CONECT 632 630 -CONECT 633 630 634 647 -CONECT 634 633 635 636 +CONECT 633 630 634 634 647 +CONECT 634 633 633 635 636 CONECT 635 634 CONECT 636 634 637 638 CONECT 637 636 -CONECT 638 636 639 647 -CONECT 639 638 640 641 +CONECT 638 636 639 639 647 +CONECT 639 638 638 640 641 CONECT 640 639 -CONECT 641 639 642 643 +CONECT 641 639 642 643 643 CONECT 642 641 -CONECT 643 641 644 645 +CONECT 643 641 641 644 645 CONECT 644 643 -CONECT 645 643 646 647 +CONECT 645 643 646 647 647 CONECT 646 645 -CONECT 647 633 638 645 -CONECT 648 628 649 650 -CONECT 649 648 +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 @@ -1509,8 +1509,8 @@ CONECT 658 656 CONECT 659 656 CONECT 660 654 661 CONECT 661 660 -CONECT 662 652 663 664 -CONECT 663 662 +CONECT 662 652 663 663 664 +CONECT 663 662 662 CONECT 664 662 665 666 CONECT 665 664 CONECT 666 664 667 668 683 @@ -1518,20 +1518,20 @@ CONECT 667 666 CONECT 668 666 669 670 671 CONECT 669 668 CONECT 670 668 -CONECT 671 668 672 681 -CONECT 672 671 673 674 +CONECT 671 668 672 672 681 +CONECT 672 671 671 673 674 CONECT 673 672 -CONECT 674 672 675 676 +CONECT 674 672 675 676 676 CONECT 675 674 -CONECT 676 674 677 679 +CONECT 676 674 674 677 679 CONECT 677 676 678 CONECT 678 677 -CONECT 679 676 680 681 +CONECT 679 676 680 681 681 CONECT 680 679 -CONECT 681 671 679 682 +CONECT 681 671 679 679 682 CONECT 682 681 -CONECT 683 666 684 685 -CONECT 684 683 +CONECT 683 666 684 684 685 +CONECT 684 683 683 CONECT 685 683 686 687 CONECT 686 685 CONECT 687 685 688 689 695 @@ -1539,11 +1539,11 @@ CONECT 688 687 CONECT 689 687 690 691 692 CONECT 690 689 CONECT 691 689 -CONECT 692 689 693 694 -CONECT 693 692 +CONECT 692 689 693 693 694 +CONECT 693 692 692 CONECT 694 692 -CONECT 695 687 696 697 -CONECT 696 695 +CONECT 695 687 696 696 697 +CONECT 696 695 695 CONECT 697 695 698 699 CONECT 698 697 CONECT 699 697 700 701 707 @@ -1551,11 +1551,11 @@ CONECT 700 699 CONECT 701 699 702 703 704 CONECT 702 701 CONECT 703 701 -CONECT 704 701 705 706 -CONECT 705 704 +CONECT 704 701 705 705 706 +CONECT 705 704 704 CONECT 706 704 -CONECT 707 699 708 709 -CONECT 708 707 +CONECT 707 699 708 708 709 +CONECT 708 707 707 CONECT 709 707 710 711 CONECT 710 709 CONECT 711 709 712 713 717 @@ -1564,8 +1564,8 @@ CONECT 713 711 714 715 716 CONECT 714 713 CONECT 715 713 CONECT 716 713 -CONECT 717 711 718 719 -CONECT 718 717 +CONECT 717 711 718 718 719 +CONECT 718 717 717 CONECT 719 717 720 721 CONECT 720 719 CONECT 721 719 722 723 731 @@ -1578,8 +1578,8 @@ CONECT 727 725 CONECT 728 725 CONECT 729 723 730 CONECT 730 729 -CONECT 731 721 732 733 -CONECT 732 731 +CONECT 731 721 732 732 733 +CONECT 732 731 731 CONECT 733 731 734 735 CONECT 734 733 CONECT 735 733 736 737 753 @@ -1600,8 +1600,8 @@ CONECT 749 746 750 751 752 CONECT 750 749 CONECT 751 749 CONECT 752 749 -CONECT 753 735 754 755 -CONECT 754 753 +CONECT 753 735 754 754 755 +CONECT 754 753 753 CONECT 755 753 756 757 CONECT 756 755 CONECT 757 755 758 759 767 @@ -1614,8 +1614,8 @@ CONECT 763 761 CONECT 764 761 CONECT 765 759 766 CONECT 766 765 -CONECT 767 757 768 769 -CONECT 768 767 +CONECT 767 757 768 768 769 +CONECT 768 767 767 CONECT 769 767 770 771 CONECT 770 769 CONECT 771 769 772 773 787 @@ -1623,19 +1623,19 @@ CONECT 772 771 CONECT 773 771 774 775 776 CONECT 774 773 CONECT 775 773 -CONECT 776 773 777 785 -CONECT 777 776 778 779 +CONECT 776 773 777 777 785 +CONECT 777 776 776 778 779 CONECT 778 777 -CONECT 779 777 780 781 +CONECT 779 777 780 781 781 CONECT 780 779 -CONECT 781 779 782 783 +CONECT 781 779 779 782 783 CONECT 782 781 -CONECT 783 781 784 785 +CONECT 783 781 784 785 785 CONECT 784 783 -CONECT 785 776 783 786 +CONECT 785 776 783 783 786 CONECT 786 785 -CONECT 787 771 788 789 -CONECT 788 787 +CONECT 787 771 788 788 789 +CONECT 788 787 787 CONECT 789 787 790 791 CONECT 790 789 CONECT 791 789 792 793 801 @@ -1648,8 +1648,8 @@ CONECT 797 795 CONECT 798 795 CONECT 799 793 800 CONECT 800 799 -CONECT 801 791 802 803 -CONECT 802 801 +CONECT 801 791 802 802 803 +CONECT 802 801 801 CONECT 803 801 804 805 CONECT 804 803 CONECT 805 803 806 807 817 @@ -1664,8 +1664,8 @@ CONECT 813 807 814 815 816 CONECT 814 813 CONECT 815 813 CONECT 816 813 -CONECT 817 805 818 819 -CONECT 818 817 +CONECT 817 805 818 818 819 +CONECT 818 817 817 CONECT 819 817 820 821 CONECT 820 819 CONECT 821 819 822 823 831 @@ -1678,8 +1678,8 @@ CONECT 827 825 CONECT 828 825 CONECT 829 823 830 CONECT 830 829 -CONECT 831 821 832 833 -CONECT 832 831 +CONECT 831 821 832 832 833 +CONECT 832 831 831 CONECT 833 831 834 835 CONECT 834 833 CONECT 835 833 836 837 846 @@ -1690,11 +1690,11 @@ CONECT 839 837 CONECT 840 837 841 842 843 CONECT 841 840 CONECT 842 840 -CONECT 843 840 844 845 -CONECT 844 843 +CONECT 843 840 844 844 845 +CONECT 844 843 843 CONECT 845 843 -CONECT 846 835 847 848 -CONECT 847 846 +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 index fe5127a..92913fa 100644 --- a/unittests/output_files/test_thr_to_his_restypeFalse.pdb +++ b/unittests/output_files/test_thr_to_his_restypeFalse.pdb @@ -1,5 +1,5 @@ COMPND MET -AUTHOR GENERATED BY OPEN BABEL 2.4.1 +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 @@ -23,17 +23,17 @@ 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 21.318 26.610 21.383 1.00 0.00 H -ATOM 25 HB3 HP3 A 2 20.066 27.157 20.243 1.00 0.00 H -ATOM 26 CG HP3 A 2 21.914 26.698 19.383 1.00 0.00 C -ATOM 27 ND1 HP3 A 2 23.187 26.196 19.539 1.00 0.00 N -ATOM 28 HD1 HP3 A 2 23.686 26.156 20.416 1.00 0.00 H -ATOM 29 CE1 HP3 A 2 23.641 25.784 18.368 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 26.000 17.459 1.00 0.00 N -ATOM 32 HE2 HP3 A 2 22.778 25.785 16.475 1.00 0.00 H -ATOM 33 CD2 HP3 A 2 21.619 26.571 18.067 1.00 0.00 C -ATOM 34 HD2 HP3 A 2 20.738 26.828 17.478 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 @@ -253,8 +253,8 @@ 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 O -ATOM 255 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O +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 @@ -310,8 +310,8 @@ 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 O -ATOM 312 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O +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 @@ -348,8 +348,8 @@ 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 O -ATOM 350 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O +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 @@ -407,8 +407,8 @@ 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 O -ATOM 409 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O +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 @@ -561,8 +561,8 @@ 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 O -ATOM 563 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O +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 @@ -610,8 +610,8 @@ 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 O -ATOM 612 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O +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 @@ -632,8 +632,8 @@ 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 O -ATOM 634 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O +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 @@ -703,8 +703,8 @@ 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 O -ATOM 705 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O +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 @@ -715,8 +715,8 @@ 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 O -ATOM 717 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O +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 @@ -854,11 +854,11 @@ 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 O -ATOM 856 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O +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 O -ATOM 859 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O +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 @@ -876,26 +876,26 @@ CONECT 14 13 15 16 17 CONECT 15 14 CONECT 16 14 CONECT 17 14 -CONECT 18 5 19 20 -CONECT 19 18 +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 24 25 26 22 +CONECT 23 22 24 25 26 CONECT 24 23 CONECT 25 23 -CONECT 26 23 27 33 +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 31 34 +CONECT 33 26 26 31 34 CONECT 34 33 CONECT 35 22 -CONECT 36 22 37 38 -CONECT 37 36 +CONECT 36 22 37 37 38 +CONECT 37 36 36 CONECT 38 36 39 40 CONECT 39 38 CONECT 40 38 41 42 57 @@ -903,20 +903,20 @@ CONECT 41 40 CONECT 42 40 43 44 45 CONECT 43 42 CONECT 44 42 -CONECT 45 42 46 55 -CONECT 46 45 47 48 +CONECT 45 42 46 46 55 +CONECT 46 45 45 47 48 CONECT 47 46 -CONECT 48 46 49 50 +CONECT 48 46 49 50 50 CONECT 49 48 -CONECT 50 48 51 53 +CONECT 50 48 48 51 53 CONECT 51 50 52 CONECT 52 51 -CONECT 53 50 54 55 +CONECT 53 50 54 55 55 CONECT 54 53 -CONECT 55 45 53 56 +CONECT 55 45 53 53 56 CONECT 56 55 -CONECT 57 40 58 59 -CONECT 58 57 +CONECT 57 40 58 58 59 +CONECT 58 57 57 CONECT 59 57 60 61 CONECT 60 59 CONECT 61 59 62 63 79 @@ -937,8 +937,8 @@ CONECT 75 72 76 77 78 CONECT 76 75 CONECT 77 75 CONECT 78 75 -CONECT 79 61 80 81 -CONECT 80 79 +CONECT 79 61 80 80 81 +CONECT 80 79 79 CONECT 81 79 82 83 CONECT 82 81 CONECT 83 81 84 85 98 @@ -956,8 +956,8 @@ CONECT 94 88 95 96 97 CONECT 95 94 CONECT 96 94 CONECT 97 94 -CONECT 98 83 99 100 -CONECT 99 98 +CONECT 98 83 99 99 100 +CONECT 99 98 98 CONECT 100 98 101 102 CONECT 101 100 CONECT 102 100 103 104 117 @@ -975,8 +975,8 @@ CONECT 113 110 114 115 116 CONECT 114 113 CONECT 115 113 CONECT 116 113 -CONECT 117 102 118 119 -CONECT 118 117 +CONECT 117 102 118 118 119 +CONECT 118 117 117 CONECT 119 117 120 121 CONECT 120 119 CONECT 121 119 122 123 136 @@ -994,8 +994,8 @@ CONECT 132 126 133 134 135 CONECT 133 132 CONECT 134 132 CONECT 135 132 -CONECT 136 121 137 138 -CONECT 137 136 +CONECT 136 121 137 137 138 +CONECT 137 136 136 CONECT 138 136 139 140 CONECT 139 138 CONECT 140 138 141 142 150 @@ -1003,20 +1003,20 @@ CONECT 141 140 CONECT 142 140 143 144 145 CONECT 143 142 CONECT 144 142 -CONECT 145 142 146 147 -CONECT 146 145 +CONECT 145 142 146 146 147 +CONECT 146 145 145 CONECT 147 145 148 149 CONECT 148 147 CONECT 149 147 -CONECT 150 140 151 152 -CONECT 151 150 +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 157 154 158 159 -CONECT 158 157 +CONECT 157 154 158 158 159 +CONECT 158 157 157 CONECT 159 157 160 161 CONECT 160 159 CONECT 161 159 162 163 179 @@ -1037,8 +1037,8 @@ CONECT 175 172 176 177 178 CONECT 176 175 CONECT 177 175 CONECT 178 175 -CONECT 179 161 180 181 -CONECT 180 179 +CONECT 179 161 180 180 181 +CONECT 180 179 179 CONECT 181 179 182 183 CONECT 182 181 CONECT 183 181 184 185 193 @@ -1051,8 +1051,8 @@ CONECT 189 187 CONECT 190 187 CONECT 191 185 192 CONECT 192 191 -CONECT 193 183 194 195 -CONECT 194 193 +CONECT 193 183 194 194 195 +CONECT 194 193 193 CONECT 195 193 196 197 CONECT 196 195 CONECT 197 195 198 199 212 @@ -1070,8 +1070,8 @@ CONECT 208 202 209 210 211 CONECT 209 208 CONECT 210 208 CONECT 211 208 -CONECT 212 197 213 214 -CONECT 213 212 +CONECT 212 197 213 213 214 +CONECT 213 212 212 CONECT 214 212 215 216 CONECT 215 214 CONECT 216 214 217 218 234 @@ -1092,15 +1092,15 @@ CONECT 230 227 231 232 233 CONECT 231 230 CONECT 232 230 CONECT 233 230 -CONECT 234 216 235 236 -CONECT 235 234 +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 241 238 242 243 -CONECT 242 241 +CONECT 241 238 242 242 243 +CONECT 242 241 241 CONECT 243 241 244 245 CONECT 244 243 CONECT 245 243 246 247 256 @@ -1111,11 +1111,11 @@ CONECT 249 247 CONECT 250 247 251 252 253 CONECT 251 250 CONECT 252 250 -CONECT 253 250 254 255 -CONECT 254 253 +CONECT 253 250 254 254 255 +CONECT 254 253 253 CONECT 255 253 -CONECT 256 245 257 258 -CONECT 257 256 +CONECT 256 245 257 257 258 +CONECT 257 256 256 CONECT 258 256 259 260 CONECT 259 258 CONECT 260 258 261 262 270 @@ -1128,8 +1128,8 @@ CONECT 266 264 CONECT 267 264 CONECT 268 262 269 CONECT 269 268 -CONECT 270 260 271 272 -CONECT 271 270 +CONECT 270 260 271 271 272 +CONECT 271 270 270 CONECT 272 270 273 274 CONECT 273 272 CONECT 274 272 275 276 284 @@ -1142,8 +1142,8 @@ CONECT 280 278 CONECT 281 278 CONECT 282 276 283 CONECT 283 282 -CONECT 284 274 285 286 -CONECT 285 284 +CONECT 284 274 285 285 286 +CONECT 285 284 284 CONECT 286 284 287 288 CONECT 287 286 CONECT 288 286 289 290 298 @@ -1156,8 +1156,8 @@ CONECT 294 292 CONECT 295 292 CONECT 296 290 297 CONECT 297 296 -CONECT 298 288 299 300 -CONECT 299 298 +CONECT 298 288 299 299 300 +CONECT 299 298 298 CONECT 300 298 301 302 CONECT 301 300 CONECT 302 300 303 304 313 @@ -1168,11 +1168,11 @@ CONECT 306 304 CONECT 307 304 308 309 310 CONECT 308 307 CONECT 309 307 -CONECT 310 307 311 312 -CONECT 311 310 +CONECT 310 307 311 311 312 +CONECT 311 310 310 CONECT 312 310 -CONECT 313 302 314 315 -CONECT 314 313 +CONECT 313 302 314 314 315 +CONECT 314 313 313 CONECT 315 313 316 317 CONECT 316 315 CONECT 317 315 318 319 323 @@ -1181,8 +1181,8 @@ CONECT 319 317 320 321 322 CONECT 320 319 CONECT 321 319 CONECT 322 319 -CONECT 323 317 324 325 -CONECT 324 323 +CONECT 323 317 324 324 325 +CONECT 324 323 323 CONECT 325 323 326 327 CONECT 326 325 CONECT 327 325 328 329 339 @@ -1197,8 +1197,8 @@ CONECT 335 329 336 337 338 CONECT 336 335 CONECT 337 335 CONECT 338 335 -CONECT 339 327 340 341 -CONECT 340 339 +CONECT 339 327 340 340 341 +CONECT 340 339 339 CONECT 341 339 342 343 CONECT 342 341 CONECT 343 341 344 345 351 @@ -1206,11 +1206,11 @@ CONECT 344 343 CONECT 345 343 346 347 348 CONECT 346 345 CONECT 347 345 -CONECT 348 345 349 350 -CONECT 349 348 +CONECT 348 345 349 349 350 +CONECT 349 348 348 CONECT 350 348 -CONECT 351 343 352 353 -CONECT 352 351 +CONECT 351 343 352 352 353 +CONECT 352 351 351 CONECT 353 351 354 355 CONECT 354 353 CONECT 355 353 356 357 361 @@ -1219,8 +1219,8 @@ CONECT 357 355 358 359 360 CONECT 358 357 CONECT 359 357 CONECT 360 357 -CONECT 361 355 362 363 -CONECT 362 361 +CONECT 361 355 362 362 363 +CONECT 362 361 361 CONECT 363 361 364 365 CONECT 364 363 CONECT 365 363 366 367 371 @@ -1229,8 +1229,8 @@ CONECT 367 365 368 369 370 CONECT 368 367 CONECT 369 367 CONECT 370 367 -CONECT 371 365 372 373 -CONECT 372 371 +CONECT 371 365 372 372 373 +CONECT 372 371 371 CONECT 373 371 374 375 CONECT 374 373 CONECT 375 373 376 377 385 @@ -1243,8 +1243,8 @@ CONECT 381 379 CONECT 382 379 CONECT 383 377 384 CONECT 384 383 -CONECT 385 375 386 387 -CONECT 386 385 +CONECT 385 375 386 386 387 +CONECT 386 385 385 CONECT 387 385 388 389 CONECT 388 387 CONECT 389 387 390 391 395 @@ -1253,8 +1253,8 @@ CONECT 391 389 392 393 394 CONECT 392 391 CONECT 393 391 CONECT 394 391 -CONECT 395 389 396 397 -CONECT 396 395 +CONECT 395 389 396 396 397 +CONECT 396 395 395 CONECT 397 395 398 399 CONECT 398 397 CONECT 399 397 400 401 410 @@ -1265,11 +1265,11 @@ CONECT 403 401 CONECT 404 401 405 406 407 CONECT 405 404 CONECT 406 404 -CONECT 407 404 408 409 -CONECT 408 407 +CONECT 407 404 408 408 409 +CONECT 408 407 407 CONECT 409 407 -CONECT 410 399 411 412 -CONECT 411 410 +CONECT 410 399 411 411 412 +CONECT 411 410 410 CONECT 412 410 413 414 CONECT 413 412 CONECT 414 412 415 416 432 @@ -1290,8 +1290,8 @@ CONECT 428 425 429 430 431 CONECT 429 428 CONECT 430 428 CONECT 431 428 -CONECT 432 414 433 434 -CONECT 433 432 +CONECT 432 414 433 433 434 +CONECT 433 432 432 CONECT 434 432 435 436 CONECT 435 434 CONECT 436 434 437 438 448 @@ -1306,8 +1306,8 @@ CONECT 444 438 445 446 447 CONECT 445 444 CONECT 446 444 CONECT 447 444 -CONECT 448 436 449 450 -CONECT 449 448 +CONECT 448 436 449 449 450 +CONECT 449 448 448 CONECT 450 448 451 452 CONECT 451 450 CONECT 452 450 453 454 468 @@ -1315,19 +1315,19 @@ CONECT 453 452 CONECT 454 452 455 456 457 CONECT 455 454 CONECT 456 454 -CONECT 457 454 458 466 -CONECT 458 457 459 460 +CONECT 457 454 458 458 466 +CONECT 458 457 457 459 460 CONECT 459 458 -CONECT 460 458 461 462 +CONECT 460 458 461 462 462 CONECT 461 460 -CONECT 462 460 463 464 +CONECT 462 460 460 463 464 CONECT 463 462 -CONECT 464 462 465 466 +CONECT 464 462 465 466 466 CONECT 465 464 -CONECT 466 457 464 467 +CONECT 466 457 464 464 467 CONECT 467 466 -CONECT 468 452 469 470 -CONECT 469 468 +CONECT 468 452 469 469 470 +CONECT 469 468 468 CONECT 470 468 471 472 CONECT 471 470 CONECT 472 470 473 474 490 @@ -1348,8 +1348,8 @@ CONECT 486 483 487 488 489 CONECT 487 486 CONECT 488 486 CONECT 489 486 -CONECT 490 472 491 492 -CONECT 491 490 +CONECT 490 472 491 491 492 +CONECT 491 490 490 CONECT 492 490 493 494 CONECT 493 492 CONECT 494 492 495 496 507 @@ -1360,13 +1360,13 @@ CONECT 498 496 CONECT 499 496 500 501 502 CONECT 500 499 CONECT 501 499 -CONECT 502 499 503 504 -CONECT 503 502 +CONECT 502 499 503 503 504 +CONECT 503 502 502 CONECT 504 502 505 506 CONECT 505 504 CONECT 506 504 -CONECT 507 494 508 509 -CONECT 508 507 +CONECT 507 494 508 508 509 +CONECT 508 507 507 CONECT 509 507 510 511 CONECT 510 509 CONECT 511 509 512 513 528 @@ -1374,20 +1374,20 @@ CONECT 512 511 CONECT 513 511 514 515 516 CONECT 514 513 CONECT 515 513 -CONECT 516 513 517 526 -CONECT 517 516 518 519 +CONECT 516 513 517 517 526 +CONECT 517 516 516 518 519 CONECT 518 517 -CONECT 519 517 520 521 +CONECT 519 517 520 521 521 CONECT 520 519 -CONECT 521 519 522 524 +CONECT 521 519 519 522 524 CONECT 522 521 523 CONECT 523 522 -CONECT 524 521 525 526 +CONECT 524 521 525 526 526 CONECT 525 524 -CONECT 526 516 524 527 +CONECT 526 516 524 524 527 CONECT 527 526 -CONECT 528 511 529 530 -CONECT 529 528 +CONECT 528 511 529 529 530 +CONECT 529 528 528 CONECT 530 528 531 532 CONECT 531 530 CONECT 532 530 533 534 538 @@ -1396,8 +1396,8 @@ CONECT 534 532 535 536 537 CONECT 535 534 CONECT 536 534 CONECT 537 534 -CONECT 538 532 539 540 -CONECT 539 538 +CONECT 538 532 539 539 540 +CONECT 539 538 538 CONECT 540 538 541 542 CONECT 541 540 CONECT 542 540 543 544 552 @@ -1405,13 +1405,13 @@ CONECT 543 542 CONECT 544 542 545 546 547 CONECT 545 544 CONECT 546 544 -CONECT 547 544 548 549 -CONECT 548 547 +CONECT 547 544 548 548 549 +CONECT 548 547 547 CONECT 549 547 550 551 CONECT 550 549 CONECT 551 549 -CONECT 552 542 553 554 -CONECT 553 552 +CONECT 552 542 553 553 554 +CONECT 553 552 552 CONECT 554 552 555 556 CONECT 555 554 CONECT 556 554 557 558 564 @@ -1419,11 +1419,11 @@ CONECT 557 556 CONECT 558 556 559 560 561 CONECT 559 558 CONECT 560 558 -CONECT 561 558 562 563 -CONECT 562 561 +CONECT 561 558 562 562 563 +CONECT 562 561 561 CONECT 563 561 -CONECT 564 556 565 566 -CONECT 565 564 +CONECT 564 556 565 565 566 +CONECT 565 564 564 CONECT 566 564 567 568 CONECT 567 566 CONECT 568 566 569 570 578 @@ -1431,20 +1431,20 @@ CONECT 569 568 CONECT 570 568 571 572 573 CONECT 571 570 CONECT 572 570 -CONECT 573 570 574 575 -CONECT 574 573 +CONECT 573 570 574 574 575 +CONECT 574 573 573 CONECT 575 573 576 577 CONECT 576 575 CONECT 577 575 -CONECT 578 568 579 580 -CONECT 579 578 +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 585 582 586 587 -CONECT 586 585 +CONECT 585 582 586 586 587 +CONECT 586 585 585 CONECT 587 585 588 589 CONECT 588 587 CONECT 589 587 590 591 601 @@ -1459,8 +1459,8 @@ CONECT 597 591 598 599 600 CONECT 598 597 CONECT 599 597 CONECT 600 597 -CONECT 601 589 602 603 -CONECT 602 601 +CONECT 601 589 602 602 603 +CONECT 602 601 601 CONECT 603 601 604 605 CONECT 604 603 CONECT 605 603 606 607 613 @@ -1468,18 +1468,18 @@ CONECT 606 605 CONECT 607 605 608 609 610 CONECT 608 607 CONECT 609 607 -CONECT 610 607 611 612 -CONECT 611 610 +CONECT 610 607 611 611 612 +CONECT 611 610 610 CONECT 612 610 -CONECT 613 605 614 615 -CONECT 614 613 +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 620 617 621 622 -CONECT 621 620 +CONECT 620 617 621 621 622 +CONECT 621 620 620 CONECT 622 620 623 624 CONECT 623 622 CONECT 624 622 625 626 635 @@ -1490,11 +1490,11 @@ CONECT 628 626 CONECT 629 626 630 631 632 CONECT 630 629 CONECT 631 629 -CONECT 632 629 633 634 -CONECT 633 632 +CONECT 632 629 633 633 634 +CONECT 633 632 632 CONECT 634 632 -CONECT 635 624 636 637 -CONECT 636 635 +CONECT 635 624 636 636 637 +CONECT 636 635 635 CONECT 637 635 638 639 CONECT 638 637 CONECT 639 637 640 641 659 @@ -1502,23 +1502,23 @@ CONECT 640 639 CONECT 641 639 642 643 644 CONECT 642 641 CONECT 643 641 -CONECT 644 641 645 658 -CONECT 645 644 646 647 +CONECT 644 641 645 645 658 +CONECT 645 644 644 646 647 CONECT 646 645 CONECT 647 645 648 649 CONECT 648 647 -CONECT 649 647 650 658 -CONECT 650 649 651 652 +CONECT 649 647 650 650 658 +CONECT 650 649 649 651 652 CONECT 651 650 -CONECT 652 650 653 654 +CONECT 652 650 653 654 654 CONECT 653 652 -CONECT 654 652 655 656 +CONECT 654 652 652 655 656 CONECT 655 654 -CONECT 656 654 657 658 +CONECT 656 654 657 658 658 CONECT 657 656 -CONECT 658 644 649 656 -CONECT 659 639 660 661 -CONECT 660 659 +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 @@ -1531,8 +1531,8 @@ CONECT 669 667 CONECT 670 667 CONECT 671 665 672 CONECT 672 671 -CONECT 673 663 674 675 -CONECT 674 673 +CONECT 673 663 674 674 675 +CONECT 674 673 673 CONECT 675 673 676 677 CONECT 676 675 CONECT 677 675 678 679 694 @@ -1540,20 +1540,20 @@ CONECT 678 677 CONECT 679 677 680 681 682 CONECT 680 679 CONECT 681 679 -CONECT 682 679 683 692 -CONECT 683 682 684 685 +CONECT 682 679 683 683 692 +CONECT 683 682 682 684 685 CONECT 684 683 -CONECT 685 683 686 687 +CONECT 685 683 686 687 687 CONECT 686 685 -CONECT 687 685 688 690 +CONECT 687 685 685 688 690 CONECT 688 687 689 CONECT 689 688 -CONECT 690 687 691 692 +CONECT 690 687 691 692 692 CONECT 691 690 -CONECT 692 682 690 693 +CONECT 692 682 690 690 693 CONECT 693 692 -CONECT 694 677 695 696 -CONECT 695 694 +CONECT 694 677 695 695 696 +CONECT 695 694 694 CONECT 696 694 697 698 CONECT 697 696 CONECT 698 696 699 700 706 @@ -1561,11 +1561,11 @@ CONECT 699 698 CONECT 700 698 701 702 703 CONECT 701 700 CONECT 702 700 -CONECT 703 700 704 705 -CONECT 704 703 +CONECT 703 700 704 704 705 +CONECT 704 703 703 CONECT 705 703 -CONECT 706 698 707 708 -CONECT 707 706 +CONECT 706 698 707 707 708 +CONECT 707 706 706 CONECT 708 706 709 710 CONECT 709 708 CONECT 710 708 711 712 718 @@ -1573,11 +1573,11 @@ CONECT 711 710 CONECT 712 710 713 714 715 CONECT 713 712 CONECT 714 712 -CONECT 715 712 716 717 -CONECT 716 715 +CONECT 715 712 716 716 717 +CONECT 716 715 715 CONECT 717 715 -CONECT 718 710 719 720 -CONECT 719 718 +CONECT 718 710 719 719 720 +CONECT 719 718 718 CONECT 720 718 721 722 CONECT 721 720 CONECT 722 720 723 724 728 @@ -1586,8 +1586,8 @@ CONECT 724 722 725 726 727 CONECT 725 724 CONECT 726 724 CONECT 727 724 -CONECT 728 722 729 730 -CONECT 729 728 +CONECT 728 722 729 729 730 +CONECT 729 728 728 CONECT 730 728 731 732 CONECT 731 730 CONECT 732 730 733 734 742 @@ -1600,8 +1600,8 @@ CONECT 738 736 CONECT 739 736 CONECT 740 734 741 CONECT 741 740 -CONECT 742 732 743 744 -CONECT 743 742 +CONECT 742 732 743 743 744 +CONECT 743 742 742 CONECT 744 742 745 746 CONECT 745 744 CONECT 746 744 747 748 764 @@ -1622,8 +1622,8 @@ CONECT 760 757 761 762 763 CONECT 761 760 CONECT 762 760 CONECT 763 760 -CONECT 764 746 765 766 -CONECT 765 764 +CONECT 764 746 765 765 766 +CONECT 765 764 764 CONECT 766 764 767 768 CONECT 767 766 CONECT 768 766 769 770 778 @@ -1636,8 +1636,8 @@ CONECT 774 772 CONECT 775 772 CONECT 776 770 777 CONECT 777 776 -CONECT 778 768 779 780 -CONECT 779 778 +CONECT 778 768 779 779 780 +CONECT 779 778 778 CONECT 780 778 781 782 CONECT 781 780 CONECT 782 780 783 784 798 @@ -1645,19 +1645,19 @@ CONECT 783 782 CONECT 784 782 785 786 787 CONECT 785 784 CONECT 786 784 -CONECT 787 784 788 796 -CONECT 788 787 789 790 +CONECT 787 784 788 788 796 +CONECT 788 787 787 789 790 CONECT 789 788 -CONECT 790 788 791 792 +CONECT 790 788 791 792 792 CONECT 791 790 -CONECT 792 790 793 794 +CONECT 792 790 790 793 794 CONECT 793 792 -CONECT 794 792 795 796 +CONECT 794 792 795 796 796 CONECT 795 794 -CONECT 796 787 794 797 +CONECT 796 787 794 794 797 CONECT 797 796 -CONECT 798 782 799 800 -CONECT 799 798 +CONECT 798 782 799 799 800 +CONECT 799 798 798 CONECT 800 798 801 802 CONECT 801 800 CONECT 802 800 803 804 812 @@ -1670,8 +1670,8 @@ CONECT 808 806 CONECT 809 806 CONECT 810 804 811 CONECT 811 810 -CONECT 812 802 813 814 -CONECT 813 812 +CONECT 812 802 813 813 814 +CONECT 813 812 812 CONECT 814 812 815 816 CONECT 815 814 CONECT 816 814 817 818 828 @@ -1686,8 +1686,8 @@ CONECT 824 818 825 826 827 CONECT 825 824 CONECT 826 824 CONECT 827 824 -CONECT 828 816 829 830 -CONECT 829 828 +CONECT 828 816 829 829 830 +CONECT 829 828 828 CONECT 830 828 831 832 CONECT 831 830 CONECT 832 830 833 834 842 @@ -1700,8 +1700,8 @@ CONECT 838 836 CONECT 839 836 CONECT 840 834 841 CONECT 841 840 -CONECT 842 832 843 844 -CONECT 843 842 +CONECT 842 832 843 843 844 +CONECT 843 842 842 CONECT 844 842 845 846 CONECT 845 844 CONECT 846 844 847 848 857 @@ -1712,11 +1712,11 @@ CONECT 850 848 CONECT 851 848 852 853 854 CONECT 852 851 CONECT 853 851 -CONECT 854 851 855 856 -CONECT 855 854 +CONECT 854 851 855 855 856 +CONECT 855 854 854 CONECT 856 854 -CONECT 857 846 858 859 -CONECT 858 857 +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 index ae067fc..20a1049 100644 --- a/unittests/output_files/test_thr_to_his_restypeTrue.pdb +++ b/unittests/output_files/test_thr_to_his_restypeTrue.pdb @@ -1,5 +1,5 @@ COMPND MET -AUTHOR GENERATED BY OPEN BABEL 2.4.1 +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 @@ -23,17 +23,17 @@ 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 21.318 26.610 21.383 1.00 0.00 H -ATOM 25 HB3 HIP A 2 20.066 27.157 20.243 1.00 0.00 H -ATOM 26 CG HIP A 2 21.914 26.698 19.383 1.00 0.00 C -ATOM 27 ND1 HIP A 2 23.187 26.196 19.539 1.00 0.00 N -ATOM 28 HD1 HIP A 2 23.686 26.156 20.416 1.00 0.00 H -ATOM 29 CE1 HIP A 2 23.641 25.784 18.368 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 26.000 17.459 1.00 0.00 N -ATOM 32 HE2 HIP A 2 22.778 25.785 16.475 1.00 0.00 H -ATOM 33 CD2 HIP A 2 21.619 26.571 18.067 1.00 0.00 C -ATOM 34 HD2 HIP A 2 20.738 26.828 17.478 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 @@ -253,8 +253,8 @@ 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 O -ATOM 255 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O +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 @@ -310,8 +310,8 @@ 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 O -ATOM 312 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O +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 @@ -348,8 +348,8 @@ 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 O -ATOM 350 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O +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 @@ -407,8 +407,8 @@ 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 O -ATOM 409 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O +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 @@ -561,8 +561,8 @@ 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 O -ATOM 563 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O +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 @@ -610,8 +610,8 @@ 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 O -ATOM 612 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O +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 @@ -632,8 +632,8 @@ 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 O -ATOM 634 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O +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 @@ -703,8 +703,8 @@ 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 O -ATOM 705 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O +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 @@ -715,8 +715,8 @@ 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 O -ATOM 717 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O +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 @@ -854,11 +854,11 @@ 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 O -ATOM 856 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O +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 O -ATOM 859 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O +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 @@ -876,26 +876,26 @@ CONECT 14 13 15 16 17 CONECT 15 14 CONECT 16 14 CONECT 17 14 -CONECT 18 5 19 20 -CONECT 19 18 +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 24 25 26 22 +CONECT 23 22 24 25 26 CONECT 24 23 CONECT 25 23 -CONECT 26 23 27 33 +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 31 34 +CONECT 33 26 26 31 34 CONECT 34 33 CONECT 35 22 -CONECT 36 22 37 38 -CONECT 37 36 +CONECT 36 22 37 37 38 +CONECT 37 36 36 CONECT 38 36 39 40 CONECT 39 38 CONECT 40 38 41 42 57 @@ -903,20 +903,20 @@ CONECT 41 40 CONECT 42 40 43 44 45 CONECT 43 42 CONECT 44 42 -CONECT 45 42 46 55 -CONECT 46 45 47 48 +CONECT 45 42 46 46 55 +CONECT 46 45 45 47 48 CONECT 47 46 -CONECT 48 46 49 50 +CONECT 48 46 49 50 50 CONECT 49 48 -CONECT 50 48 51 53 +CONECT 50 48 48 51 53 CONECT 51 50 52 CONECT 52 51 -CONECT 53 50 54 55 +CONECT 53 50 54 55 55 CONECT 54 53 -CONECT 55 45 53 56 +CONECT 55 45 53 53 56 CONECT 56 55 -CONECT 57 40 58 59 -CONECT 58 57 +CONECT 57 40 58 58 59 +CONECT 58 57 57 CONECT 59 57 60 61 CONECT 60 59 CONECT 61 59 62 63 79 @@ -937,8 +937,8 @@ CONECT 75 72 76 77 78 CONECT 76 75 CONECT 77 75 CONECT 78 75 -CONECT 79 61 80 81 -CONECT 80 79 +CONECT 79 61 80 80 81 +CONECT 80 79 79 CONECT 81 79 82 83 CONECT 82 81 CONECT 83 81 84 85 98 @@ -956,8 +956,8 @@ CONECT 94 88 95 96 97 CONECT 95 94 CONECT 96 94 CONECT 97 94 -CONECT 98 83 99 100 -CONECT 99 98 +CONECT 98 83 99 99 100 +CONECT 99 98 98 CONECT 100 98 101 102 CONECT 101 100 CONECT 102 100 103 104 117 @@ -975,8 +975,8 @@ CONECT 113 110 114 115 116 CONECT 114 113 CONECT 115 113 CONECT 116 113 -CONECT 117 102 118 119 -CONECT 118 117 +CONECT 117 102 118 118 119 +CONECT 118 117 117 CONECT 119 117 120 121 CONECT 120 119 CONECT 121 119 122 123 136 @@ -994,8 +994,8 @@ CONECT 132 126 133 134 135 CONECT 133 132 CONECT 134 132 CONECT 135 132 -CONECT 136 121 137 138 -CONECT 137 136 +CONECT 136 121 137 137 138 +CONECT 137 136 136 CONECT 138 136 139 140 CONECT 139 138 CONECT 140 138 141 142 150 @@ -1003,20 +1003,20 @@ CONECT 141 140 CONECT 142 140 143 144 145 CONECT 143 142 CONECT 144 142 -CONECT 145 142 146 147 -CONECT 146 145 +CONECT 145 142 146 146 147 +CONECT 146 145 145 CONECT 147 145 148 149 CONECT 148 147 CONECT 149 147 -CONECT 150 140 151 152 -CONECT 151 150 +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 157 154 158 159 -CONECT 158 157 +CONECT 157 154 158 158 159 +CONECT 158 157 157 CONECT 159 157 160 161 CONECT 160 159 CONECT 161 159 162 163 179 @@ -1037,8 +1037,8 @@ CONECT 175 172 176 177 178 CONECT 176 175 CONECT 177 175 CONECT 178 175 -CONECT 179 161 180 181 -CONECT 180 179 +CONECT 179 161 180 180 181 +CONECT 180 179 179 CONECT 181 179 182 183 CONECT 182 181 CONECT 183 181 184 185 193 @@ -1051,8 +1051,8 @@ CONECT 189 187 CONECT 190 187 CONECT 191 185 192 CONECT 192 191 -CONECT 193 183 194 195 -CONECT 194 193 +CONECT 193 183 194 194 195 +CONECT 194 193 193 CONECT 195 193 196 197 CONECT 196 195 CONECT 197 195 198 199 212 @@ -1070,8 +1070,8 @@ CONECT 208 202 209 210 211 CONECT 209 208 CONECT 210 208 CONECT 211 208 -CONECT 212 197 213 214 -CONECT 213 212 +CONECT 212 197 213 213 214 +CONECT 213 212 212 CONECT 214 212 215 216 CONECT 215 214 CONECT 216 214 217 218 234 @@ -1092,15 +1092,15 @@ CONECT 230 227 231 232 233 CONECT 231 230 CONECT 232 230 CONECT 233 230 -CONECT 234 216 235 236 -CONECT 235 234 +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 241 238 242 243 -CONECT 242 241 +CONECT 241 238 242 242 243 +CONECT 242 241 241 CONECT 243 241 244 245 CONECT 244 243 CONECT 245 243 246 247 256 @@ -1111,11 +1111,11 @@ CONECT 249 247 CONECT 250 247 251 252 253 CONECT 251 250 CONECT 252 250 -CONECT 253 250 254 255 -CONECT 254 253 +CONECT 253 250 254 254 255 +CONECT 254 253 253 CONECT 255 253 -CONECT 256 245 257 258 -CONECT 257 256 +CONECT 256 245 257 257 258 +CONECT 257 256 256 CONECT 258 256 259 260 CONECT 259 258 CONECT 260 258 261 262 270 @@ -1128,8 +1128,8 @@ CONECT 266 264 CONECT 267 264 CONECT 268 262 269 CONECT 269 268 -CONECT 270 260 271 272 -CONECT 271 270 +CONECT 270 260 271 271 272 +CONECT 271 270 270 CONECT 272 270 273 274 CONECT 273 272 CONECT 274 272 275 276 284 @@ -1142,8 +1142,8 @@ CONECT 280 278 CONECT 281 278 CONECT 282 276 283 CONECT 283 282 -CONECT 284 274 285 286 -CONECT 285 284 +CONECT 284 274 285 285 286 +CONECT 285 284 284 CONECT 286 284 287 288 CONECT 287 286 CONECT 288 286 289 290 298 @@ -1156,8 +1156,8 @@ CONECT 294 292 CONECT 295 292 CONECT 296 290 297 CONECT 297 296 -CONECT 298 288 299 300 -CONECT 299 298 +CONECT 298 288 299 299 300 +CONECT 299 298 298 CONECT 300 298 301 302 CONECT 301 300 CONECT 302 300 303 304 313 @@ -1168,11 +1168,11 @@ CONECT 306 304 CONECT 307 304 308 309 310 CONECT 308 307 CONECT 309 307 -CONECT 310 307 311 312 -CONECT 311 310 +CONECT 310 307 311 311 312 +CONECT 311 310 310 CONECT 312 310 -CONECT 313 302 314 315 -CONECT 314 313 +CONECT 313 302 314 314 315 +CONECT 314 313 313 CONECT 315 313 316 317 CONECT 316 315 CONECT 317 315 318 319 323 @@ -1181,8 +1181,8 @@ CONECT 319 317 320 321 322 CONECT 320 319 CONECT 321 319 CONECT 322 319 -CONECT 323 317 324 325 -CONECT 324 323 +CONECT 323 317 324 324 325 +CONECT 324 323 323 CONECT 325 323 326 327 CONECT 326 325 CONECT 327 325 328 329 339 @@ -1197,8 +1197,8 @@ CONECT 335 329 336 337 338 CONECT 336 335 CONECT 337 335 CONECT 338 335 -CONECT 339 327 340 341 -CONECT 340 339 +CONECT 339 327 340 340 341 +CONECT 340 339 339 CONECT 341 339 342 343 CONECT 342 341 CONECT 343 341 344 345 351 @@ -1206,11 +1206,11 @@ CONECT 344 343 CONECT 345 343 346 347 348 CONECT 346 345 CONECT 347 345 -CONECT 348 345 349 350 -CONECT 349 348 +CONECT 348 345 349 349 350 +CONECT 349 348 348 CONECT 350 348 -CONECT 351 343 352 353 -CONECT 352 351 +CONECT 351 343 352 352 353 +CONECT 352 351 351 CONECT 353 351 354 355 CONECT 354 353 CONECT 355 353 356 357 361 @@ -1219,8 +1219,8 @@ CONECT 357 355 358 359 360 CONECT 358 357 CONECT 359 357 CONECT 360 357 -CONECT 361 355 362 363 -CONECT 362 361 +CONECT 361 355 362 362 363 +CONECT 362 361 361 CONECT 363 361 364 365 CONECT 364 363 CONECT 365 363 366 367 371 @@ -1229,8 +1229,8 @@ CONECT 367 365 368 369 370 CONECT 368 367 CONECT 369 367 CONECT 370 367 -CONECT 371 365 372 373 -CONECT 372 371 +CONECT 371 365 372 372 373 +CONECT 372 371 371 CONECT 373 371 374 375 CONECT 374 373 CONECT 375 373 376 377 385 @@ -1243,8 +1243,8 @@ CONECT 381 379 CONECT 382 379 CONECT 383 377 384 CONECT 384 383 -CONECT 385 375 386 387 -CONECT 386 385 +CONECT 385 375 386 386 387 +CONECT 386 385 385 CONECT 387 385 388 389 CONECT 388 387 CONECT 389 387 390 391 395 @@ -1253,8 +1253,8 @@ CONECT 391 389 392 393 394 CONECT 392 391 CONECT 393 391 CONECT 394 391 -CONECT 395 389 396 397 -CONECT 396 395 +CONECT 395 389 396 396 397 +CONECT 396 395 395 CONECT 397 395 398 399 CONECT 398 397 CONECT 399 397 400 401 410 @@ -1265,11 +1265,11 @@ CONECT 403 401 CONECT 404 401 405 406 407 CONECT 405 404 CONECT 406 404 -CONECT 407 404 408 409 -CONECT 408 407 +CONECT 407 404 408 408 409 +CONECT 408 407 407 CONECT 409 407 -CONECT 410 399 411 412 -CONECT 411 410 +CONECT 410 399 411 411 412 +CONECT 411 410 410 CONECT 412 410 413 414 CONECT 413 412 CONECT 414 412 415 416 432 @@ -1290,8 +1290,8 @@ CONECT 428 425 429 430 431 CONECT 429 428 CONECT 430 428 CONECT 431 428 -CONECT 432 414 433 434 -CONECT 433 432 +CONECT 432 414 433 433 434 +CONECT 433 432 432 CONECT 434 432 435 436 CONECT 435 434 CONECT 436 434 437 438 448 @@ -1306,8 +1306,8 @@ CONECT 444 438 445 446 447 CONECT 445 444 CONECT 446 444 CONECT 447 444 -CONECT 448 436 449 450 -CONECT 449 448 +CONECT 448 436 449 449 450 +CONECT 449 448 448 CONECT 450 448 451 452 CONECT 451 450 CONECT 452 450 453 454 468 @@ -1315,19 +1315,19 @@ CONECT 453 452 CONECT 454 452 455 456 457 CONECT 455 454 CONECT 456 454 -CONECT 457 454 458 466 -CONECT 458 457 459 460 +CONECT 457 454 458 458 466 +CONECT 458 457 457 459 460 CONECT 459 458 -CONECT 460 458 461 462 +CONECT 460 458 461 462 462 CONECT 461 460 -CONECT 462 460 463 464 +CONECT 462 460 460 463 464 CONECT 463 462 -CONECT 464 462 465 466 +CONECT 464 462 465 466 466 CONECT 465 464 -CONECT 466 457 464 467 +CONECT 466 457 464 464 467 CONECT 467 466 -CONECT 468 452 469 470 -CONECT 469 468 +CONECT 468 452 469 469 470 +CONECT 469 468 468 CONECT 470 468 471 472 CONECT 471 470 CONECT 472 470 473 474 490 @@ -1348,8 +1348,8 @@ CONECT 486 483 487 488 489 CONECT 487 486 CONECT 488 486 CONECT 489 486 -CONECT 490 472 491 492 -CONECT 491 490 +CONECT 490 472 491 491 492 +CONECT 491 490 490 CONECT 492 490 493 494 CONECT 493 492 CONECT 494 492 495 496 507 @@ -1360,13 +1360,13 @@ CONECT 498 496 CONECT 499 496 500 501 502 CONECT 500 499 CONECT 501 499 -CONECT 502 499 503 504 -CONECT 503 502 +CONECT 502 499 503 503 504 +CONECT 503 502 502 CONECT 504 502 505 506 CONECT 505 504 CONECT 506 504 -CONECT 507 494 508 509 -CONECT 508 507 +CONECT 507 494 508 508 509 +CONECT 508 507 507 CONECT 509 507 510 511 CONECT 510 509 CONECT 511 509 512 513 528 @@ -1374,20 +1374,20 @@ CONECT 512 511 CONECT 513 511 514 515 516 CONECT 514 513 CONECT 515 513 -CONECT 516 513 517 526 -CONECT 517 516 518 519 +CONECT 516 513 517 517 526 +CONECT 517 516 516 518 519 CONECT 518 517 -CONECT 519 517 520 521 +CONECT 519 517 520 521 521 CONECT 520 519 -CONECT 521 519 522 524 +CONECT 521 519 519 522 524 CONECT 522 521 523 CONECT 523 522 -CONECT 524 521 525 526 +CONECT 524 521 525 526 526 CONECT 525 524 -CONECT 526 516 524 527 +CONECT 526 516 524 524 527 CONECT 527 526 -CONECT 528 511 529 530 -CONECT 529 528 +CONECT 528 511 529 529 530 +CONECT 529 528 528 CONECT 530 528 531 532 CONECT 531 530 CONECT 532 530 533 534 538 @@ -1396,8 +1396,8 @@ CONECT 534 532 535 536 537 CONECT 535 534 CONECT 536 534 CONECT 537 534 -CONECT 538 532 539 540 -CONECT 539 538 +CONECT 538 532 539 539 540 +CONECT 539 538 538 CONECT 540 538 541 542 CONECT 541 540 CONECT 542 540 543 544 552 @@ -1405,13 +1405,13 @@ CONECT 543 542 CONECT 544 542 545 546 547 CONECT 545 544 CONECT 546 544 -CONECT 547 544 548 549 -CONECT 548 547 +CONECT 547 544 548 548 549 +CONECT 548 547 547 CONECT 549 547 550 551 CONECT 550 549 CONECT 551 549 -CONECT 552 542 553 554 -CONECT 553 552 +CONECT 552 542 553 553 554 +CONECT 553 552 552 CONECT 554 552 555 556 CONECT 555 554 CONECT 556 554 557 558 564 @@ -1419,11 +1419,11 @@ CONECT 557 556 CONECT 558 556 559 560 561 CONECT 559 558 CONECT 560 558 -CONECT 561 558 562 563 -CONECT 562 561 +CONECT 561 558 562 562 563 +CONECT 562 561 561 CONECT 563 561 -CONECT 564 556 565 566 -CONECT 565 564 +CONECT 564 556 565 565 566 +CONECT 565 564 564 CONECT 566 564 567 568 CONECT 567 566 CONECT 568 566 569 570 578 @@ -1431,20 +1431,20 @@ CONECT 569 568 CONECT 570 568 571 572 573 CONECT 571 570 CONECT 572 570 -CONECT 573 570 574 575 -CONECT 574 573 +CONECT 573 570 574 574 575 +CONECT 574 573 573 CONECT 575 573 576 577 CONECT 576 575 CONECT 577 575 -CONECT 578 568 579 580 -CONECT 579 578 +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 585 582 586 587 -CONECT 586 585 +CONECT 585 582 586 586 587 +CONECT 586 585 585 CONECT 587 585 588 589 CONECT 588 587 CONECT 589 587 590 591 601 @@ -1459,8 +1459,8 @@ CONECT 597 591 598 599 600 CONECT 598 597 CONECT 599 597 CONECT 600 597 -CONECT 601 589 602 603 -CONECT 602 601 +CONECT 601 589 602 602 603 +CONECT 602 601 601 CONECT 603 601 604 605 CONECT 604 603 CONECT 605 603 606 607 613 @@ -1468,18 +1468,18 @@ CONECT 606 605 CONECT 607 605 608 609 610 CONECT 608 607 CONECT 609 607 -CONECT 610 607 611 612 -CONECT 611 610 +CONECT 610 607 611 611 612 +CONECT 611 610 610 CONECT 612 610 -CONECT 613 605 614 615 -CONECT 614 613 +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 620 617 621 622 -CONECT 621 620 +CONECT 620 617 621 621 622 +CONECT 621 620 620 CONECT 622 620 623 624 CONECT 623 622 CONECT 624 622 625 626 635 @@ -1490,11 +1490,11 @@ CONECT 628 626 CONECT 629 626 630 631 632 CONECT 630 629 CONECT 631 629 -CONECT 632 629 633 634 -CONECT 633 632 +CONECT 632 629 633 633 634 +CONECT 633 632 632 CONECT 634 632 -CONECT 635 624 636 637 -CONECT 636 635 +CONECT 635 624 636 636 637 +CONECT 636 635 635 CONECT 637 635 638 639 CONECT 638 637 CONECT 639 637 640 641 659 @@ -1502,23 +1502,23 @@ CONECT 640 639 CONECT 641 639 642 643 644 CONECT 642 641 CONECT 643 641 -CONECT 644 641 645 658 -CONECT 645 644 646 647 +CONECT 644 641 645 645 658 +CONECT 645 644 644 646 647 CONECT 646 645 CONECT 647 645 648 649 CONECT 648 647 -CONECT 649 647 650 658 -CONECT 650 649 651 652 +CONECT 649 647 650 650 658 +CONECT 650 649 649 651 652 CONECT 651 650 -CONECT 652 650 653 654 +CONECT 652 650 653 654 654 CONECT 653 652 -CONECT 654 652 655 656 +CONECT 654 652 652 655 656 CONECT 655 654 -CONECT 656 654 657 658 +CONECT 656 654 657 658 658 CONECT 657 656 -CONECT 658 644 649 656 -CONECT 659 639 660 661 -CONECT 660 659 +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 @@ -1531,8 +1531,8 @@ CONECT 669 667 CONECT 670 667 CONECT 671 665 672 CONECT 672 671 -CONECT 673 663 674 675 -CONECT 674 673 +CONECT 673 663 674 674 675 +CONECT 674 673 673 CONECT 675 673 676 677 CONECT 676 675 CONECT 677 675 678 679 694 @@ -1540,20 +1540,20 @@ CONECT 678 677 CONECT 679 677 680 681 682 CONECT 680 679 CONECT 681 679 -CONECT 682 679 683 692 -CONECT 683 682 684 685 +CONECT 682 679 683 683 692 +CONECT 683 682 682 684 685 CONECT 684 683 -CONECT 685 683 686 687 +CONECT 685 683 686 687 687 CONECT 686 685 -CONECT 687 685 688 690 +CONECT 687 685 685 688 690 CONECT 688 687 689 CONECT 689 688 -CONECT 690 687 691 692 +CONECT 690 687 691 692 692 CONECT 691 690 -CONECT 692 682 690 693 +CONECT 692 682 690 690 693 CONECT 693 692 -CONECT 694 677 695 696 -CONECT 695 694 +CONECT 694 677 695 695 696 +CONECT 695 694 694 CONECT 696 694 697 698 CONECT 697 696 CONECT 698 696 699 700 706 @@ -1561,11 +1561,11 @@ CONECT 699 698 CONECT 700 698 701 702 703 CONECT 701 700 CONECT 702 700 -CONECT 703 700 704 705 -CONECT 704 703 +CONECT 703 700 704 704 705 +CONECT 704 703 703 CONECT 705 703 -CONECT 706 698 707 708 -CONECT 707 706 +CONECT 706 698 707 707 708 +CONECT 707 706 706 CONECT 708 706 709 710 CONECT 709 708 CONECT 710 708 711 712 718 @@ -1573,11 +1573,11 @@ CONECT 711 710 CONECT 712 710 713 714 715 CONECT 713 712 CONECT 714 712 -CONECT 715 712 716 717 -CONECT 716 715 +CONECT 715 712 716 716 717 +CONECT 716 715 715 CONECT 717 715 -CONECT 718 710 719 720 -CONECT 719 718 +CONECT 718 710 719 719 720 +CONECT 719 718 718 CONECT 720 718 721 722 CONECT 721 720 CONECT 722 720 723 724 728 @@ -1586,8 +1586,8 @@ CONECT 724 722 725 726 727 CONECT 725 724 CONECT 726 724 CONECT 727 724 -CONECT 728 722 729 730 -CONECT 729 728 +CONECT 728 722 729 729 730 +CONECT 729 728 728 CONECT 730 728 731 732 CONECT 731 730 CONECT 732 730 733 734 742 @@ -1600,8 +1600,8 @@ CONECT 738 736 CONECT 739 736 CONECT 740 734 741 CONECT 741 740 -CONECT 742 732 743 744 -CONECT 743 742 +CONECT 742 732 743 743 744 +CONECT 743 742 742 CONECT 744 742 745 746 CONECT 745 744 CONECT 746 744 747 748 764 @@ -1622,8 +1622,8 @@ CONECT 760 757 761 762 763 CONECT 761 760 CONECT 762 760 CONECT 763 760 -CONECT 764 746 765 766 -CONECT 765 764 +CONECT 764 746 765 765 766 +CONECT 765 764 764 CONECT 766 764 767 768 CONECT 767 766 CONECT 768 766 769 770 778 @@ -1636,8 +1636,8 @@ CONECT 774 772 CONECT 775 772 CONECT 776 770 777 CONECT 777 776 -CONECT 778 768 779 780 -CONECT 779 778 +CONECT 778 768 779 779 780 +CONECT 779 778 778 CONECT 780 778 781 782 CONECT 781 780 CONECT 782 780 783 784 798 @@ -1645,19 +1645,19 @@ CONECT 783 782 CONECT 784 782 785 786 787 CONECT 785 784 CONECT 786 784 -CONECT 787 784 788 796 -CONECT 788 787 789 790 +CONECT 787 784 788 788 796 +CONECT 788 787 787 789 790 CONECT 789 788 -CONECT 790 788 791 792 +CONECT 790 788 791 792 792 CONECT 791 790 -CONECT 792 790 793 794 +CONECT 792 790 790 793 794 CONECT 793 792 -CONECT 794 792 795 796 +CONECT 794 792 795 796 796 CONECT 795 794 -CONECT 796 787 794 797 +CONECT 796 787 794 794 797 CONECT 797 796 -CONECT 798 782 799 800 -CONECT 799 798 +CONECT 798 782 799 799 800 +CONECT 799 798 798 CONECT 800 798 801 802 CONECT 801 800 CONECT 802 800 803 804 812 @@ -1670,8 +1670,8 @@ CONECT 808 806 CONECT 809 806 CONECT 810 804 811 CONECT 811 810 -CONECT 812 802 813 814 -CONECT 813 812 +CONECT 812 802 813 813 814 +CONECT 813 812 812 CONECT 814 812 815 816 CONECT 815 814 CONECT 816 814 817 818 828 @@ -1686,8 +1686,8 @@ CONECT 824 818 825 826 827 CONECT 825 824 CONECT 826 824 CONECT 827 824 -CONECT 828 816 829 830 -CONECT 829 828 +CONECT 828 816 829 829 830 +CONECT 829 828 828 CONECT 830 828 831 832 CONECT 831 830 CONECT 832 830 833 834 842 @@ -1700,8 +1700,8 @@ CONECT 838 836 CONECT 839 836 CONECT 840 834 841 CONECT 841 840 -CONECT 842 832 843 844 -CONECT 843 842 +CONECT 842 832 843 843 844 +CONECT 843 842 842 CONECT 844 842 845 846 CONECT 845 844 CONECT 846 844 847 848 857 @@ -1712,11 +1712,11 @@ CONECT 850 848 CONECT 851 848 852 853 854 CONECT 852 851 CONECT 853 851 -CONECT 854 851 855 856 -CONECT 855 854 +CONECT 854 851 855 855 856 +CONECT 855 854 854 CONECT 856 854 -CONECT 857 846 858 859 -CONECT 858 857 +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 index 228f350..16eab6a 100755 --- a/unittests/run_unitests.sh +++ b/unittests/run_unitests.sh @@ -11,4 +11,6 @@ source /home/duerr/miniconda3/bin/activate openmm export PYTHONPATH=/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/:$PYTHONPATH -python -m unittest discover . +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 index 96beaba..b248ce7 100644 --- a/unittests/test_StartGA_Run.py +++ b/unittests/test_StartGA_Run.py @@ -8,7 +8,7 @@ ''' import unittest -import openbabel +from openbabel import openbabel from src import JobConfig from src.gaapi import operator_types from src.gaapi import generators @@ -73,6 +73,7 @@ def test_general_loading(self): 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) @@ -97,8 +98,10 @@ def test_initPop_helicalstability(self): 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==1604: + if lineno==1606: + final_energy=float(line[10:26]) f.close() @@ -125,7 +128,7 @@ def read_atom_lines(infile): # 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) @@ -150,6 +153,7 @@ def test_initPop_helicalstability_openmm(self): 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) diff --git a/unittests/test_openbabel.py b/unittests/test_openbabel.py index f182fab..ed146bb 100644 --- a/unittests/test_openbabel.py +++ b/unittests/test_openbabel.py @@ -155,7 +155,7 @@ class DemoSettings(object): except: print("test_swap could not be deleted.") - @unittest.skip("see if this one fails") + #@unittest.skip("see if this one fails") def test_MoleculeCreator_glycine(self): class DemoSettings(object):