AMBER force field parameters of 160 organic molecules for MD simulations using GROMACS

Published: 2 March 2021| Version 3 | DOI: 10.17632/phxtv76n5s.3


General AMBER force field (GAFF) parameters are provided for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. The parameters were determined based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory using Gaussian 09. For each molecule a coordinate file of the three-dimensional molecular structure, the topology and the parameter file are provided. The applicability of these parameters was demonstrated by MD simulations for each of these molecules.using Gromacs 2018. All Gaussian 09 and Gromacs 2018 input files are provided too, along with example bash scripts for how to invoke these programs.


Steps to reproduce

Quantum mechanics (QM) at the HF6-31G* level of theory using Gaussian, explicit-solvent molecular dynamics (MD) simulations using Gromacs


Obafemi Awolowo University, Forschungszentrum Julich GmbH, Heinrich Heine Universitat Dusseldorf Mathematisch-Naturwissenschaftliche Fakultat


Drug Discovery, Molecular Dynamics, Computational Chemistry