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PsiRESP

😪-RESP

Latest release PyPI version Documentation Status
Status GH Actions Status codecov Language grade: Python
Community License: LGPL v3

PsiRESP is a package for calculating atomic partial charges from restrained and unrestrained electrostatic potential fits using Psi4. It is highly flexible, configurable, easy to use, and totally written in Python. It supports fitting to multiple orientations and conformers, as well as both intra-molecular and inter-molecular charge constraints for multi-molecule fits. It is written to correspond closely with existing tools such as the RESP ESP charge Derive (R.E.D.) tools.

As of now, the following implementations are well-tested to reproduce results from existing tools, primarily R.E.D.:

  • standard 2-stage RESP (convenience class: psiresp.configs.TwoStageRESP)
  • standard 1-stage RESP (convenience class: psiresp.configs.OneStageRESP)
  • standard unrestrained ESP (convenience class: psiresp.configs.ESP)

These implementations are not as well-tested:

  • ESP using HF/STO-3G (convenience class: psiresp.configs.WeinerESP) -- Psi4 seems to minimize to a relatively different geometry than GAMESS with STO-3G.
  • psiresp.configs.ATBRESP, mimicking the method used by the Automated Topology Builder is not tested at all. The published methods do not indicate the point density, moreover, the results generated seem to have changed since the original paper. Use at your own risk.
  • psiresp.configs.RESP2, as the methods are expensive

Installation

Create a new conda environment with dependencies. In general, installing the dependencies required will be difficult without conda, as both Psi4 and RDKit are most easily distributed through conda.

conda env create -f devtools/conda-envs/environment.yaml
conda activate psiresp

To install the latest release:

pip install psiresp

Alternatively, to build from source, clone this repository and install the package.

git clone https://github.com/lilyminium/psiresp.git
cd psiresp
python setup.py install

Please see the Installation docs for more information on installation and dependencies.

Example

For example, running a standard 2-stage restrained electrostatic potential fit (Bayly et al., 1993) as standard in AMBER (implemented as RESP-A1 in R.E.D.):

   import psiresp
   from psiresp.testing import FractalSnowflake  # if using Jupyter, use FractalSnowflakeHandler below
   # from qcfractal import FractalSnowflakeHandler
   import qcfractal.interface as ptl

   # set up server and client
   server = FractalSnowflake()
   client = ptl.FractalClient(server)

   # set up conformer generation options
   conformer_options = psiresp.ConformerGenerationOptions(n_max_conformers=2)  # generate at most 2 conformers
   
   # set up molecule
   dmso = psiresp.Molecule.from_smiles("CS(=O)C", charge=0, multiplicity=1,
                                       optimize_geometry=True,  # optimize conformers
                                       conformer_generation_options=conformer_options
                                       )
      
   # set up charge constraints
   charge_constraints = psiresp.ChargeConstraintOptions(
      symmetric_methyls=True,  # make methyl Hs around carbons the same charge
      symmetric_methylenes=True,  # make methylene Hs around carbons the same charge
   )
   # constrain S and O atoms to sum to -0.19617
   so_atoms = dmso.get_atoms_from_smarts("S=O")[0]
   charge_constraints.add_charge_sum_constraint(charge=-0.19617, atoms=so_atoms)
   # constrain two C atoms to have the same charge
   cc_atoms = dmso.get_atoms_from_smarts("[C:1]S(=O)[C:2]")[0]
   charge_constraints.add_charge_equivalence_constraint(atoms=cc_atoms)
   
   # set up job
   job = psiresp.Job(
      molecules=[dmso],
      resp_options=psiresp.RespOptions(
         stage_2=True,  # run 2-stage RESP
         restraint_height_stage_1=0.0005,  # hyperbola restraints for stage 1
         restraint_height_stage_2=0.001,  # hyperbola restraints for stage 2
         restrained_fit=True,  # restrain ESP fit
      ),
      qm_optimization_options=psiresp.QMGeometryOptimizationOptions(
         basis="6-31g*",
         method="hf",
      ),
      qm_esp_options=psiresp.QMEnergyOptions(
         basis="6-31g*",
         method="hf",
      ),
      charge_constraints=charge_constraints,
   )

   charges = job.run(client=client)

Alternatively, use the preconfigured TwoStageRESP class in psiresp.configs. This sets up the grid_options, resp_options, qm_optimization_options, and qm_esp_options

   job = psiresp.TwoStageRESP(molecules=[dmso])
   # constrain S and O atoms to sum to -0.19617
   so_atoms = dmso.get_atoms_from_smarts("S=O")[0]
   job.charge_constraints.add_charge_sum_constraint(charge=-0.19617, atoms=so_atoms)
   # constrain two C atoms to have the same charge
   cc_atoms = dmso.get_atoms_from_smarts("[C:1]S(=O)[C:2]")[0]
   job.charge_constraints.add_charge_equivalence_constraint(atoms=cc_atoms)

   charges = job.run()

Please see the examples and documentation for more.

Copyright

Copyright (c) 2020, Lily Wang

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.2.

Pre-configured models and reorientation algorithm are written to directly match results from RESP ESP charge Derive (R.E.D.). Dupradeau, F.-Y. et al. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. Phys. Chem. Chem. Phys. 12, 7821 (2010).

ATBRESP tries to match results from Automated Topology Builder (A.T.B.). Malde, A. K. et al. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. J. Chem. Theory Comput. 7, 4026–4037 (2011).

RESP2 tries to match results from RESP2. Schauperl, M. et al. Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2). Commun Chem 3, 1–11 (2020).

Some tests compare results to output from resp, the current RESP plugin for Psi4. Alenaizan, A., Burns, L. A. & Sherrill, C. D. Python implementation of the restrained electrostatic potential charge model. International Journal of Quantum Chemistry 120, e26035 (2020).

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