title: Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field.
abstract: In this study, we propose newly derived parameters for phosphate ions in the context of the GROMOS force field parameter sets. The non-bonded parameters used up to now lead to a hydration free energy, which renders the dihydrogen phosphate ion too hydrophobic when compared to experimentally derived values, making a reparametrization of the phosphate moiety necessary. Phosphate species are of great importance in biomolecular simulations not only because of their crucial role in the backbone of nucleic acids but also as they represent one of the most important types of post-translational modifications to protein side-chains and are an integral part in many lipids. Our re-parametrization of the free dihydrogen phosphate (H 2PO 4-) and three derivatives (methyl phosphate, dimethyl phosphate, and phenyl phosphate) leads, in conjunction with the previously updated charged side-chains in the GROMOS parameter set 54A8, to new nucleic acid backbone parameters and a 54A8 version of the widely used GROMOS protein post-translational modification parameter set. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Margreitter
authors.affiliation: Physics Department T38, Technical University of Munich, Munich, Germany.
authors.forename: Maria M
authors.initials: MM
authors.lastname: Reif
authors.affiliation: Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria.
authors.forename: Chris
authors.identifier: 0000-0002-4232-2556
authors.initials: C
authors.lastname: Oostenbrink
keywords: force-field; molecular dynamics; parametrization; phosphates; post-translational modifications; solvation free energies