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 [email protected]
Baofeng Zhang [email protected]
Rajat Pal [email protected]
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 openmm, configobj and numpy python modules.
conda create -n atm -c conda-forge ambertools openmm openmm-atmmetaforce-plugin configobj setproctitle r-base
git clone https://github.com/Gallicchio-Lab/AToM-OpenMM.git
cd AToM-OpenMM
python setup.py install
Rscript -e 'install.packages("UWHAM", repos = "http://cran.us.r-project.org")'
setproctitle above is optional but useful to track the names of the processes started by AToM-OpenMM. The ambertools package is not an actual dependency but it is needed to set up some of the systems in the examples. r-base, and the UWHAM R package is required for free energy estimation. 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