RESP Library is a repository for calculating and distributing partial charges for molecular simulations with the restrained electrostatic potential (RESP) and RESP2 methods. The goal is to provide a growing library of molecules already-computed charges so that there is greater consistency and reproducibility of the partial charges used in molecular simulations.
RESP Library is in early development (0.x releases). The API may change unexpectedly.
There are a few ways to use RESP Library. If the molecule that you
are interested in already exists, you can simply take the charges
as provided in resp_library/lib/{molecule_name} and proceed. Molecules
are listed by their IUPAC name (where spaces have been replaced by
underscores. Charges are provided from the original method
(RESP1) and the new RESP2 method. There is also a way to
query the library:
import resp_library
smiles = "CC"
rdmol = resp_library.retrieve_charges(smiles, "RESP1")
for atom in rdmol.GetAtoms():
print(f"{atom.GetSymbol()}: {atom.GetProp('q')}")The retrieve_charges method returns an rdkit molecule with the
partial charges specified as the atomic property q. If the molecule
does not yet exist in resp_library, a RESPLibraryError is raised.
In this case, you can compute the charges for a new molecule and add them to the RESP Library with a pull request. This is a two-step procedure. First, you setup the calculation as follows:
import resp_library
smiles = "CCO"
resp_library.prepare_charge_calculation(smiles)This creates a new directory with the IUPAC name corresponding
to the SMILES string under resp_library/lib. The IUPAC name
is autogenerated from the SMILES string from the
NIH CACTUS
server. Two subdirectories are created, RESP1 and RESP2.
Inside of each, you will find a resp.yaml file. This file is
mostly completed, but you will need to edit the charge_constraints
and equality constraints to be correct for your molecule.
The RESP procedure specifies that charge equality be enforced
for symmetric groups and that the charges of polar centers and
attached hydrogens be fixed for the second round of the RESP calculation.
These two sections of the YAML file are used to specify these
constraints. For example, in the case of ethanol, the oxygen
and hydrogen bonded to oxygen would be constrained in the second-stage
fitting, the 3 hydrogens bound to the first aliphatic carbon are
constrained to have the same charge, and the two hydrogens bound to
the middle carbon are constrained to have the same charge.
Therefore, that section of the yaml file would be edited to become:
charge_constraints:
- [3] # O
- [9] # H
equality_constraints:
- [4, 5, 6] # H, H, H
- [7, 8] # H, HThe file resp_library/lib/{molecule_name}/template.pdb is generated
by prepare_charge_calculation to provide the atom ordering.
The atom numbering in the YAML file is 1-indexed. The other line of the
YAML file that may need to be edited is the number of conformers
to be generated; if the molecule has less than 5 atoms you should reduce
this number from 5 to 2. rdkit will not be able to generate enough
distinct conformers for very small molecules.
After updating the YAML files you may run the charge calculations. Depending on the size of the molecule this may take some time.
import resp_library
resp_library.calculate_charges("CCO", "RESP1")
resp_library.calculate_charges("CCO", "RESP2")Unless you see errors, it is likely that the charge calculation was
successful. The charges can be found under
resp_library/lib/{molecule_name}/RESP1/results and
resp_library/lib/{molecule_name}/RESP2/results. The RESP2
charges include both vacuum and implicit solvent (pcm) results.
To add the charges to the library, add and commit the new directory to a branch. For example:
git checkout -b add/ethanol
git add resp_library/ethanol/*
git commit -m "Add ethanol to RESP library"RESP charges are only reliable to ~0.01q. Therefore, we provided
rounded charges in the results folder. However, sometimes,
during the charge rounding, the symmetry specified in the YAML
file is broken. Please check and fix any broken symmetry manually
while preserving the net charge of the molecule. These changes
should be added as a second commit to clearly document the
manual modifications.
Currently, installation from source is the only option.
We recommend creating a conda environment to manage the
depenedencies. Some dependencies are only available via pip.
Note that it is important to do an editable installation
from your fork of the repository if you plan on adding
to the RESP library.
git clone [email protected]/rsdefever/resp_library.git
cd resp_library
conda create --name resp_lib --file requirements-conda.txt -c psi4/label/dev -c conda-forge
conda activate resp_lib
pip install -r requirements-pip.txt
pip install -e .Development of RESP Library was supported by the National Science Foundation under grant NSF Grant Number 1835874. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.