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.
AToM uses the ATMetaForce plugin for OpenMM.
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).
Authors:
Emilio Gallicchio egallicchio@brooklyn.cuny.edu
Baofeng Zhang BZhang@brooklyn.cuny.edu
Rajat Pal rajatfor2014@gmail.com
The asynchronous replica exchange method was first implemented in the AsyncRE package for the IMPACT program.
Please cite us if you use this software in your research:
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Alchemical Transfer Approach to Absolute Binding Free Energy Estimation
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Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing
It is recommended that the installation is performed in a personal python environment (conda, miniconda, or similar). AToM requires the configobj and numpy python modules.
conda create -n atm -c conda-forge openmm-atmmetaforce-plugin configobj
git clone https://github.com/Gallicchio-Lab/AToM-OpenMM.git
cd AToM-OpenMM
python setup.py install
See examples for examples and tutorials.
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 is provided without any guarantees of correctness. Please report issues here. We welcome contributions and pull requests.
This software is licensed under the terms of the GNU General Public License. See LICENSE