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Eur Biophys J. 2011 Jul;40(7):843-56. doi: 10.1007/s00249-011-0700-9. Epub 2011 Apr 30.

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

Author information

1
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zürich, Switzerland.

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.

PMID:
21533652
DOI:
10.1007/s00249-011-0700-9
[Indexed for MEDLINE]

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