assign_v2.py: A Numbering System for Palladium Molecular Dynamics Simulations

Introduction

assign_v2.py is a software developed to derive a novel force field for molecular dynamics simulations of square planar palladium compounds using a unique "numbering system" technique. This system addresses the challenge of varying bond angles in cis-trans isomers of palladium compounds.

Prerequisites

Before running the program, ensure the following:

1. The atom definitions, especially those labeled with numbers like 1c, 2n, 3o, and any atom starting with a number from the file PARMCHK.DAT, should be present in your local parmchk.dat file of the AMBER suite.
2. The parmchk2 utility should be readily accessible and callable from the command line.
3. The sander program should also be accessible from the command line.
4. Ensure environment variables are properly set, for instance, having run a command like source $AMBERHOME.

Dependencies

The software requires the following Python libraries:

• os
• sys
• subprocess
• numpy
• re
• argparse
• shutil
• logging
• itertools

Usage

1. Ensure your .mol2 file is in the same directory as assign_v2.py.
2. Run the software by providing the .mol2 file as an argument:

python3 assign_v2.py YOUR_FILENAME.mol2

After execution, assign_v2.py will generate a .frcmod file containing palladium parameters consistent with the numbering system.

Conclusion

assign_v2.py provides a novel approach to derive force fields for palladium compounds, making the previously challenging task of simulating the square planar geometry of palladium straightforward.

Citation

DOI: 10.1080/07391102.2023.2283812 PMID: 38031443 Title: "Assign_v2: a novel bonded-force field parameterization software for square planar palladium molecular dynamics simulations" Author: Barış KURT