antefoyer

This repository provides support for the General Amber Force Field (GAFF) in foyer. Foyer is a part of the Molecular Simulation Design Framework (MoSDeF). A few relevant links are provided below:

• MoSDeF
• Foyer GitHub
• Foyer paper
• GAFF paper
• Antechamber paper

There are two primary components to this repository:

• Foyer-compatible XML file for GAFF
• Antechamber wrapper to integrate antechamber atomtyping and AM1-BCC charge assignment directly into MoSDeF workflows.

Installation

The following instructions will create a new python 3.7 conda environment (antefoyer) and install the required packages and dependencies:

git clone https://github.com/rsdefever/antefoyer
conda create --name antefoyer -c conda-forge -c mosdef -c omnia python=3.7 --file antefoyer/requirements.txt
conda activate antefoyer
cd antefoyer/.
pip install . 

Dependencies

• foyer >= 0.7.4
• networkx
• ambertools (for the antefoyer.ante_atomtyping and antefoyer.ante_charges functions)

Optional dependencies

To complete some of the examples below you will need mbuild and openbabel installed. These can be added via conda:

conda install -c conda-forge mbuild openbabel

Usage

There are two primary workflows for atomtyping with antefoyer. The first uses the traditional foyer approach with SMARTS strings defined in antefoyer/xml/gaff.xml.

# Assuming we also have mbuild installed for this example
import foyer
import mbuild as mb

# Build/import a molecule
molecule = mb.load('CCC',smiles=True)

# Load GAFF
GAFF = foyer.forcefields.load_GAFF()

# Use foyer to parameterize
parameterized_molecule = GAFF.apply(molecule.to_parmed())

# Save to whatever file format you desire

Note that antefoyer was never imported. If antefoyer is properly installed, the GAFF forcefield will become available under foyer.forcefields.load_GAFF() via entrypoints.

The second workflow uses the antechamber wrapper. This requires antechamber to be installed an accesible in your PATH. Antechamber can be installed from conda: conda install -c conda-forge ambertools.

# Assuming we also have mbuild installed for this example
import foyer
import mbuild as mb

# For this we need to import antefoyer
import antefoyer

# Build/import a molecule
molecule = mb.load('CCC', smiles=True)

# Load GAFF
gaff = foyer.forcefields.load_GAFF()

# Identify GAFF atomtypes with antechamber
typed_molecule = antefoyer.ante_atomtyping(molecule, 'gaff')

# Use foyer to parameterize
parameterized_molecule = gaff.parametrize_system(typed_molecule)

# We can also apply AM1-BCC charges from antechamber
molecule_with_charges = antefoyer.ante_charges(parameterized_molecule,'bcc')

# Save to whatever file format you desire

Details of SMARTS strings development and testing

Further details of the SMARTS strings development and testing are provided in a separate repository, GAFF-Foyer.

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.

This material is based upon work supported by the National Science Foundation under Grant #1835874