PyGROMODS: a Python package for the generation of input files for molecular dynamic simulation with GROMACS

Abstract

The pyGROMODS, an easy-to-use cross-platform python-based package, with a graphical user interface, for the generation of molecular dynamic (MD) input files and running MD simulation (MDS) of proteins, peptides, and protein-ligand complex using GROMACS, is here presented. Four routes, with underlining Python scripts, are implemented in pyGROMODS for the generation of MD input files. They are ‘RLmulti’ for processing multi-ligand protein complex, ‘RLmany’ for processing multiple ligands against a single protein target, ‘RLsingle’ for processing multiple pairs of proteins and ligands, and ‘PPmore’ for processing peptides or proteins without ligands or non-standard residues. In addition, using the package, the generated input files or appropriate input files from other sources can be uploaded to run MDS with GROMACS. The pyGROMODS is implemented with a unique ability to search the host machine systems for the installation of the required software, update and/or install required Python packages, allow the user to pre-define working directory, and generate unique workflow organization with well-defined folders and files in a well-organized manner. The pyGROMODS, which is released under the MIT License, is freely available for download via the GitHub (https://github.com/Dankem/pyGROMODS) and Zenodo (https://doi.org/10.5281/zenodo.7912747) repositories. The precompiled executables can also be downloaded from Zenodo (https://doi.org/10.5281/zenodo.8087090), and a video tutorial can be downloaded from https://youtu.be/I4OKc6uVx1M. Communicated by Ramaswamy H. Sarma