acellera-atm 0.1.0

A molecule reading/writing and manipulation package.

Acellera-ATM

Acellera-ATM is an Alchemical Transfer Method (ATM) package for the Acellera platform. The implementation is based on the AToM-OpenMM codebase https://github.com/Gallicchio-Lab/AToM-OpenMM by Emilio Gallicchio's lab.

Installation and usage

You can install the Acellera-ATM package via conda or pip. To use conda you need a working conda installation, we recommend using the Miniforge package for this.

Once conda is installed, you can install the Acellera-ATM package with the following command:

conda create -n atm -y # Create a new conda environment
conda activate atm     # Activate the environment
conda install acellera-atm python=3.10 -c acellera -c conda-forge # Install the package

Usage

To use the Acellera-ATM package, you can either use it from command line or from python. You can follow the tutorial here to get started.

Citations

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

• Alchemical Transfer Approach to Absolute Binding Free Energy Estimation

• Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing