pyGROMODS

pyGROMODS generates MD input files and prepares molecular systems for GROMACS molecular dynamics simulations.

Key Features:

• Multiple Processing Routes: Four Python scripts are provided: RLmulti processes multi-ligand protein complexes; RLmany handles multiple ligands against a single protein target; RLsingle manages multiple protein–ligand pairs; and PPmore processes peptides or proteins without ligands or non-standard residues.
• MD Input Generation: Produces MD input files intended for use with GROMACS molecular dynamics simulations.
• Integration with GROMACS: Generates input files compatible with GROMACS for running molecular dynamics simulations.
• Workflow Organization: Pre-defines working directories and organizes workflows into structured folders and files.
• Software Management: Searches the host system for installed software, updates Python packages, and installs missing Python packages as required.

Scientific Applications:

• Molecular dynamics simulations of biomolecules: Preparation of input files and system setups for MD studies of proteins, peptides, and ligand-containing complexes in computational biology and bioinformatics.

Methodology:

Generates MD input files via four Python scripts (RLmulti, RLmany, RLsingle, PPmore), organizes working directories and workflow files, manages Python/software installations, and outputs input compatible with GROMACS.