easyPARM v4.00: A Python-based tool for the automated parameterization of metalloproteins and metal-organic polyhedra...

Force-field parameters for classical molecular dynamics simulations of metal centers are often derived from electronic structure calculations due to the inexistence of transferable libraries. Metalloproteins and metal-organic polyhedrons systems add more layers of complexity with respect to molecular transition metal complexes due to the usual presence of multiple metal cores and the coordination with amino acids of the protein and/or non-standard structures, forcing user intervention and making the parameterization process very tedious, time-demanding, and prone to errors. This work presents easyPARM v4.00, a Python-based tool that allows the automated parameterization of these (multi)metallic systems, strongly minimizing human intervention and computational cost. Additional implementations like compatibility with the GAMESS-US software and the non-interactive mode are explained in detail, whereas the quality of the obtained parameters is systematically validated against reference data (including density functional theory molecular dynamics), fully demonstrating that the proposed procedure is not only streamlined but also reliable and versatile. The code is distributed as open source and free of charge on GitHub at https://github.com/Abdelazim-Abdelgawwad/easyPARM.git.