PDB2DAT: Automating LAMMPS data file generation from PDB molecular systems using Python, Rdkit, and Pysimm

Abstract

Pdb2dat, developed in Python, is an open-source, self-contained utility that facilitates the conversion of PDB files into LAMMPS data files, catering to the need of initializing atomistic simulation from initial atomic configurations. It extracts molecular details from PDB files, uses Rdkit and Xyz2mol for bonding analysis and 3D conformer generation, and uses Pysimm for assigning force field types and charges. Designed to be lightweight and fully Pythonic, pdb2dat is suitable for use in privilege-limited high-throughput environments. The output details system topologies for use in MD simulations, significantly simplifying the preparatory steps needed by researchers to explore materials phenomena through LAMMPS. • Pdb2dat converts PDB files into LAMMPS data files, preparing molecular models for use in atomistic simulations. • It integrates Rdkit and XYZ2MOL to generate molecular conformers, and Pysimm for assigning force field types and charges. • Self-contained and lightweight, requiring only standard Python libraries, making it well-suited for HPC environments. • Supports multiple force fields including CHARMM, Gaff, Gaff2, Pcff, and Tip3p, catering to diverse simulation needs. • Automatically parses atomic configurations into LAMMPS, enabling the rapid preparation of multiple MD systems effortlessly.