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 uses the ATMForce potential in the 8.1.0beta version of OpenMM sources.
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).
Maintainers:
- Emilio Gallicchio egallicchio@brooklyn.cuny.edu
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:
-
Alchemical Transfer Approach to Absolute Binding Free Energy Estimation
-
Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing
It is recommended that the installation is performed in a personal python environment (miniforge, 1miniconda, conda, or similar). AToM-OpenMM requires the openmm, configobj and numpy python modules.
This version of AToM-OpenMM requires the latest 8.1.1 version of OpenMM. This conda command installs the necessary requirements:
conda create -n atm8.1.1 -c conda-forge openmm=8.1.1 ambertools openmmforcefields configobj setproctitle r-base
conda activate atm8.1.1
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. openmmforcefields is used for force field parameter assignments using OpenFF. r-base with the UWHAM R package (see below) is required for free energy estimation. See examples for examples and tutorials.
Finally, install AToM-OpenMM:
wget https://github.com/Gallicchio-Lab/AToM-OpenMM/archive/refs/tags/v8.1.1.tar.gz
tar zxvf v8.1.1.tar.gz
cd AToM-OpenMM-8.1.1
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.
See examples for examples and tutorials.
This software is licensed under the terms of the GNU General Public License. See LICENSE
