Fixed RESP for 2-atom molecules

docs/source/examples.rst

@@ -6,9 +6,11 @@ Examples
 This is extended desription of the examples provided in metallicious package (see `examples <https://github.com/tkpiskorz/metallicious/tree/main/metallicious/examples>`_)
 
 
-Example 1: Quick start (see `example_1/ <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example1_quick_start>`_)
+Example 1: Quick start
 ------------
 
+(see `example_1/ <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example1_quick_start>`_)
+
 Simple parametrization of the cage with two metals. As input, we provide a coordination file in PDB format and non-bonded
 force-field parameters in *.top format (GROMACS). Moreover, LJ parameters of the Ru and Pd are taken from the universal force-field
 (vdw_type='uff'), as Ru is available only in this library.
@@ -21,9 +23,12 @@ force-field parameters in *.top format (GROMACS). Moreover, LJ parameters of the
     cage.parametrize(out_coord='out.pdb', out_topol='out.top')
 
 
-Example 2a: Automated initial force-field parameters (see `example_2/ <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example2_no_topology>`_) If the force-field parameters are missing, the linker(s) can be parametrized using AmberTools with a GAFF force field.
+Example 2a: Automated initial force-field parameters
 ------------
 
+(see `example_2/ <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example2_no_topology>`_)
+
+If the force-field parameters are missing, the linker(s) can be parametrized using AmberTools with a GAFF force field.
 *metallicious* will prepare the non-bonded force-field parameters of the whole structure, which are saved to the folder "init_topol."
 
 .. code-block:: python
@@ -55,9 +60,11 @@ Alternatively, you prepare_initial_topology can be specified in .parametrize:
     cage.parametrize(out_coord='out.inpcrd', out_topol='out.prmtop', prepare_initial_topology=True)
 
 
-Example 3: Homoleptic cage (see `example_3/ <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example3_only_linker_topology>`_)
+Example 3: Homoleptic cage
 ------------
 
+(see `example_3/ <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example3_only_linker_topology>`_)
+
 In the case of homoleptic cages (all linkers are the same), *metallicious* can use force-field parameters of single linker,
 which will be used to generate the initial topology of the whole structure:
 
@@ -97,9 +104,11 @@ Two solutions are available:
 1. Create a new template, which is automated but time-consuming
 2. use truncation schemes, which are fast but with reduced accuracy (caution is also needed)
 
-Example 4: Parametrization of new template (see `example_4/ <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example4_template_parametrization>`_)
+Example 4: Parametrization of new template
 ------------
 
+(see `example_4/ <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example4_template_parametrization>`_)
+
 If template parameters are unavailable, one may want to parametrize them. In *metallicious*, this is done by
 specifying the multiplicity of the metal, which signals *metallicious* to perform QM calculations if necessary. For this functionality, the additional
 dependencies (see installation guide) are needed (`autode <https://github.com/duartegroup/autodE>`_, `ORCA <https://orcaforum.kofo.mpg.de/app.php/portal>`_, and `psiRESP <https://github.com/lilyminium/psiresp>`_).
@@ -134,9 +143,10 @@ which can be changed by specifying "keywords" in the supramolecular_structure cl
     cage.parametrize(out_coord='out.pdb', out_topol='out.top', prepare_initial_topology=True)
 
 
-Example 5: Truncation schemes (see `example_5/ https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example5_truncation_scheme`_)
+Example 5: Truncation schemes
 ------------
 
+(see `example_5/ https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/example5_truncation_scheme`_)
 
 Truncation schemes allow the "recycling" of existing templates from the library by reducing their size, which might match the metal site of interest.
 Three schemes are available, cutting the template at a distance of 3-bond, 2-bond, and 1-bond from the metal centre.

docs/source/tutorials.rst

@@ -95,76 +95,95 @@ This requires only change of the library_directory, as there are no templates in
 Tutorial 5: GROMACS tutorial for MD simulations of metallorganic structures from scratch
 -----------
 
-
-This tutorial will guide you how to perform whole MD simulations from scratch. We will simulate a Ga4L6 cage in water.
-Firstly, let's do the topology of the cage from *.xyz structure:
+This tutorial will guide you in performing an MD simulation from scratch. We will simulate a Fujita's Pd4L6 cage in water.
+The files needed for this tutorial are available `here <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/tutorial5/tutorial.zip>`_.
+Firstly, let's do the topology of the cage from *.xyz structure using metallicious:
 
 .. code-block:: python
     from metallicious import supramolecular_structure
     cage = supramolecular_structure('cage_start.pdb', metal_charges={'Pd': 2}, LJ_type='uff')
     cage.parametrize(out_coord='0_cage.pdb', out_topol='topol.top', prepare_initial_topology=True)
 
 
-Execule the program:
+Execute the program:
 
 .. code-block:: bash
 
     python script.py
 
-With the topology read, let's setup the system. Firstly let's modify the size of the simulation box:
+With the topology read, we will set up the system. Firstly, let's modify the size of the simulation box to accommodate
+the cage (we use 2 nm from the cage to the wall of the simulation box):
 
 .. code-block:: bash
-gmx editconf -f 0_cage.pdb -d 2 -o 1_box.pdb
 
-We solvate the system with water (we usee 3-site water model):
+    gmx editconf -f 0_cage.pdb -d 2 -o 1_box.pdb
+
+We solvate the system with water (we will use a 3-site water model):
 
 .. code-block:: bash
-gmx solvate -cp 1_box.pdb -cs spc216.gro -o 2_solv.gro -p topol.top
+
+    gmx solvate -cp 1_box.pdb -cs spc216.gro -o 2_solv.gro -p topol.top
 
 Now, the topology file needs to be changed. Open the "topol.top" file. Firstly, we will change the header:
 
 .. code-block:: bash
-[ defaults ]
-; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
-1               2               yes             0.5          0.833333
 
-to:
+    [ defaults ]
+    ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+    1               2               yes             0.5          0.833333
 
-#include "amber99sb-ildn.ff/forcefield.itp"
+to force-field parameters, which include atom types of water:
+
+.. code-block:: bash
+
+    #include "amber99sb-ildn.ff/forcefield.itp"
+
+This will include all LJ parameters for atoms (including solvent and ions). Next, add information about the force-field
+parameters for water and ions just under the section "[ atomtypes ]" (just
+before the first [ moleculetype ]). In this case, we will use SPC/E water model:
+
+.. code-block:: bash
 
-This will include all LJ paramters for atoms (including solvent and ions). Under the section "[ atomtypes ]" (just
-before first [ moleculetype ]) we add information about the force-field paramters for water and ions topology.
-In this case we will use SPC/E water model:
+    #include "amber99sb-ildn.ff/spce.itp"
+    #include "amber99sb-ildn.ff/ions.itp"
 
-#include "amber99sb-ildn.ff/spce.itp"
-#include "amber99sb-ildn.ff/ions.itp"
+Now, we need to add ions. Firstly, we need to create a *.tpr file:
 
-Now we need to add ions. Firstly, we need to create a tpr file
+.. code-block:: bash
 
+    gmx grompp -f em.mdp -c 2_solv.gro -p topol.top -o ions.tpr -maxwarn  2
 
-gmx grompp -f em.mdp -c 2_solv.gro -p topol.top -o ions.tpr -maxwarn  2
+Then, let's add ions:
 
-Then you add ions:
+.. code-block:: bash
 
-gmx genion -s ions.tpr -o 3_ions.gro -p topol.top -pname NA -nname CL -neutral
+    gmx genion -s ions.tpr -o 3_ions.gro -p topol.top -pname NA -nname CL -neutral
 
 Select "SOL" to replace bulk water with the counterions.
-We minimize the created system (to "remove bad contacts") by firstly creating *tpr file, and then performing miniization.
+We minimize the created system (to "remove bad contacts") by making a *.tpr file and then performing minimization.
 
-gmx grompp -f em.mdp -c 3_ions.gro -p topol.top -o 4_em.tpr
-gmx mdrun -v -deffnm 4_em
+.. code-block:: bash
 
-Equilibration using NVT and NPT:
+    gmx grompp -f em.mdp -c 3_ions.gro -p topol.top -o 4_em.tpr
+    gmx mdrun -v -deffnm 4_em
 
-gmx grompp -f nvt.mdp -c 4_em.gro -p topol.top -o 5_nvt.tpr
-gmx mdrun -v -deffnm 5_nvt
+We equilibrate system using NVT and NPT ensemble:
+
+.. code-block:: bash
 
-gmx grompp -f npt.mdp -c 5_nvt.gro -p topol.top -o 6_npt.tpr
-gmx mdrun -v -deffnm 6_npt
+    gmx grompp -f nvt.mdp -c 4_em.gro -p topol.top -o 5_nvt.tpr
+    gmx mdrun -v -deffnm 5_nvt
+
+    gmx grompp -f npt.mdp -c 5_nvt.gro -p topol.top -o 6_npt.tpr
+    gmx mdrun -v -deffnm 6_npt
+
+Finally, we perform production run (ideally done on a performance cluster (HPC) with GPUs):
+
+.. code-block:: bash
 
-And finally production run (ideally done on high performance cluster (HPC) with GPUs):
+    gmx grompp -f run.mdp -c 6_npt.gro -p topol.top -o 7_run.tpr
+    gmx mdrun -v -deffnm 7_run
 
-gmx grompp -f run.mdp -c 6_npt.gro -p topol.top -o 7_run.tpr
-gmx mdrun -v -deffnm 7_run
 
-As result you obtaine final frame 7_run.gro and trajectory 7_run.xtc, which you can visualise using for example VMD.
+As a result, we should obtain the final frame 7_run.gro and trajectory 7_run.xtc, which you can visualise using a
+molecular visualization program (i.g., VMD). For your convenience, `here <https://github.com/duartegroup/metallicious/tree/main/metallicious/examples/tutorial5/final.zip>`_ are the final files compliled.

metallicious.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: metallicious
-Version: 0.2.32
+Version: 0.2.33
 License-File: LICENSE.md
 Requires-Dist: numpy
 Requires-Dist: MDAnalysis

metallicious.egg-info/SOURCES.txt

@@ -114,6 +114,8 @@ metallicious/library/Fe_2_merz-opc_3.pdb
 metallicious/library/Fe_2_merz-opc_3.top
 metallicious/library/Fe_2_uff_0.pdb
 metallicious/library/Fe_2_uff_0.top
+metallicious/library/Fe_2_uff_1.pdb
+metallicious/library/Fe_2_uff_1.top
 metallicious/library/Fe_2_zhang-opc_0.pdb
 metallicious/library/Fe_2_zhang-opc_0.top
 metallicious/library/Fe_2_zhang-opc_1.pdb

metallicious/parametrize_new_sites.py

@@ -97,7 +97,6 @@ def __init__(self, filename, metal_charge_mult=None, metal_charges=None, LJ_type
 
         elif LJ_type is None:
             for LJ_type in vdw_data:
-
                 present = [(metal_name in vdw_data[LJ_type] or f"{metal_name:}{self.metal_charge_dict[metal_name]:}" in vdw_data[LJ_type]) for metal_name in self.metal_names]
                 if sum(present) == len(present):
                     self.vdw_type = LJ_type

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "metallicious"
-version = "0.2.32"
+version = "0.2.33"
 
 dependencies = [
     "numpy",