atom-openmm 8.5.0b0

Asynchronous Replica Exchange with OpenMM

AToM-OpenMM v8.5

The Alchemical Transfer Method for OpenMM (AToM-OpenMM) is an extensible Python package for the estimation of absolute and relative binding free energies of molecular complexes. It implements the Alchemical Transfer Method (ATM) with asynchronous parallel replica exchange molecular dynamics with the OpenMM library. The AToM software can be deployed on workstations or cluster nodes with one or more GPUs.

This version of AToM-OpenMM has been tested with OpenMM 8.5 and 8.4; it uses ATMForce in the 8.4.0 or later versions of OpenMM.

Credits

This software is developed and maintained by the Emilio Gallicchio's lab with support from current and past grants from the National Science Foundation (ACI 1440665 and CHE 1750511) and the National Institutes of Health (R15 GM151708).

Maintainer/Author:

• Emilio Gallicchio [e-mail]

Contributors:

• Elian Tiudic
• Sylvester Sakyi
• Stefan Doerr
• Sheenam Khuttan
• Joe Z Wu
• Solmaz Azimi
• Baofeng Zhang
• Rajat Pal

The asynchronous replica exchange method was first implemented in the AsyncRE package for the IMPACT program.

Bibliography

Please cite us if you use this software in your research:

• Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method

• Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer with Coordinate Swapping Method

• Alchemical Transfer Approach to Absolute Binding Free Energy Estimation

• Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing

Installation & Usage

It is recommended that the installation is performed in a personal Python environment (miniforge, miniconda, conda, or similar). AToM-OpenMM requires the openmm and other Python modules.

This version of AToM-OpenMM requires OpenMM 8.4.0 or later. This conda command installs the necessary requirements:

mamba create -n atm8.5.0 -c conda-forge 'openmm>=8.4' ambertools openmmforcefields configobj setproctitle r-base espaloma
mamba activate atm8.5.0

setproctitle above is optional but useful to track the names of the processes started by AToM-OpenMM. The ambertools, openmmforcefields, and espaloma packages are not actual dependencies; they are used to prepare the molecular systems. openmmforcefields, in particular, is used to assign force field parameters using OpenFF, GAFF, or espaloma. espaloma is a machine-learning system by the Chodera lab to assign force field parameters. The r-base dependency with the UWHAM R package (see below) is required for free energy estimation in legacy workflows and will be removed in later versions. See examples for examples and tutorials.

Finally, install AToM-OpenMM:

• From the latest release:

pip install atom-openmm

• From the latest sources:

git clone https://github.com/Gallicchio-Lab/AToM-OpenMM.git
cd AToM-OpenMM
pip install .

And this will install the UWHAM R package:

Rscript -e 'install.packages("UWHAM", repos = "http://cran.us.r-project.org")' 

While we strive to develop and distribute high-quality and bug-free software, keep in mind that this is research software under heavy development. AToM-OpenMM is provided without any guarantees of correctness. Please report issues here. We welcome contributions and pull requests.

Documentation

AToM-OpenMM User Guide

AToM-OpenMM Theory Introduction

See examples for examples, workflows, and tutorials.

See example-notebooks for example Notebooks.

Licensing

This software is licensed under the terms of the GNU Lesser General Public License. See LICENSE. The AToM logo © 2023 Solmaz Azimi.