title: Definition and testing of the GROMOS force-field versions 54A7 and 54B7.
abstract: New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new φ/ψ torsional angle terms and a modification of the N-H, C=O repulsion, a new atom type for a charged -CH(3) in the choline moiety is added, the Na(+) and Cl(-) ions are modified to reproduce the free energy of hydration, and additional improper torsional angle types for free energy calculations involving a chirality change are introduced. The new helical propensity modification is tested using the benchmark proteins hen egg-white lysozyme, fox1 RNA binding domain, chorismate mutase and the GCN4-p1 peptide. The stability of the proteins is improved in comparison with the 53A6 force field, and good agreement with a range of primary experimental data is obtained.
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zürich, Switzerland.
authors.forename: Nathan
authors.initials: N
authors.lastname: Schmid
authors.forename: Andreas P
authors.initials: AP
authors.lastname: Eichenberger
authors.forename: Alexandra
authors.initials: A
authors.lastname: Choutko
authors.forename: Sereina
authors.initials: S
authors.lastname: Riniker
authors.forename: Moritz
authors.initials: M
authors.lastname: Winger
authors.forename: Alan E
authors.initials: AE
authors.lastname: Mark
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D012984:Software