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Definition and testing of the GROMOS force-field versions 54A7 and 54B7

2011; Springer Science+Business Media; Volume: 40; Issue: 7 Linguagem: Inglês

10.1007/s00249-011-0700-9

1432-1017

Nathan Schmid, Andreas P. Eichenberger, Alexandra Choutko, Sereina Riniker, Moritz Winger, Alan E. Mark, Wilfred F. van Gunsteren,

Mass Spectrometry Techniques and Applications

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 −CH3 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.