PDB2DAT

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

Journal article (2024)

Authors

E.I. Assaf Martinez-Streignard Pavement Engineering - CEG
X. Liu Pavement Engineering - CEG
Peng Lin Rijkswaterstaat
S. Erkens Rijkswaterstaat
Research Group
Pavement Engineering (CEG) (TU Delft)
Molecular dynamics Chemistry LAMMPS Atomistic simulation
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Published Date

2024

Language

English

Faculty

Civil Engineering & Geosciences

Department

Engineering Structures

Research Group

Pavement Engineering

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.