psiresp 0.0a0

psiresp

PsiRESP

😪-RESP

A RESP plugin for Psi4.

Things that probably work:

• standard 2-stage RESP, gas phase HF/6-31G* with MSK radii (convenience class: psiresp.Multi/RespA1)
• intermolecular charge constraints (use the MultiResp classes for this)
• intramolecular charge constraints (use the Resp classes for this)

Things that maybe work?

• 1-stage ESP, B3LYP/6-31G* in implicit solvent with MSK radii. Unknown point density? (convenience class: psiresp.Multi/ATBResp)
• RESP2: PW6B95/aug-cc-pV(D+d)Z in vacuum and solvent with Bondi radii, density=2.5 (convenience class: psiresp.Multi/Resp2)

Installation

To build from source, clone this repository:

git clone https://github.com/lilyminium/psiresp.git
cd psiresp

Create a new conda environment with dependencies:

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

And build the package.

python setup.py install

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 psi4
   import psiresp

   mol = psi4.Molecule.from_string("""10
      ! from R.E.D. examples/2-Dimethylsulfoxide
      C  3.87500   0.67800  -8.41700
      H  3.80000   1.69000  -8.07600
      H  3.40600   0.02600  -7.71100
      H  3.38900   0.58300  -9.36600
      S  5.35900   0.29300  -8.55900
      O  5.46000  -1.05900  -9.01400
      C  6.05500   0.43000  -7.19300
      H  7.08700   0.16300  -7.29000
      H  5.98000   1.44100  -6.85300
      H  5.58200  -0.21900  -6.48500""", fix_com=True,
      fix_orientation=True)

   r = psiresp.Resp.from_molecules([mol], charge=0, name='dmso')
   charges = r.run(stage_2=True,  # run stage 2
                   opt=True,  # geometry optimize first
                   hyp_a1=0.0005, # hyperbola restraints
                   hyp_a2=0.001,
                   restraint=True,  # restrain
                   method='hf',
                   basis='6-31g*',
                   equal_methyls=True,  # restrain methyl carbons to have the same charge
                   n_orient=2)  # automatically generate 2 molecules

Alternatively, use the preconfigured RespA1 class in psiresp.configs.

   import psi4
   import psiresp

   mol = psi4.Molecule.from_string("""10
      ! from R.E.D. examples/2-Dimethylsulfoxide
      C  3.87500   0.67800  -8.41700
      H  3.80000   1.69000  -8.07600
      H  3.40600   0.02600  -7.71100
      H  3.38900   0.58300  -9.36600
      S  5.35900   0.29300  -8.55900
      O  5.46000  -1.05900  -9.01400
      C  6.05500   0.43000  -7.19300
      H  7.08700   0.16300  -7.29000
      H  5.98000   1.44100  -6.85300
      H  5.58200  -0.21900  -6.48500""", fix_com=True,
      fix_orientation=True)

   r = psiresp.RespA1.from_molecules([mol], charge=0, name='dmso')
   charges = r.run(opt=True,  # geometry optimize first
                   equal_methyls=True,  # restrain methyl carbons to have the same charge
                   n_orient=2)  # automatically generate 2 molecules

Pre-configured models

Each of these comes with a MultiResp counterpart, although MultiATBResp and MultiResp2 are entirely untested due to the original sources not supporting intermolecular charge constraints.

Probably work:

• RespA1
• RespA2
• EspA1

Hard to test, maybe work:

• EspA2 (Psi4 minimises to quite a different geometry with HF/STO-3G compared to GAMESS)
• Resp2 (Ethanol example works; others can't say for sure, optimisation at PW6B95/aug-cc-pV(D+d)Z is so slow)
• ATBResp (Paper pretty light on details; charges produced by ATB now differ from original 2011 paper)

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).