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

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

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 −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.

Keywords

GROMOS 54A7 Force field Secondary structure 

Abbreviations

CM

Chorismate mutase

FOX

Fox1 RNA binding domain

GCN

GCN4-p1 peptide

HEWL

Hen egg-white lysozyme

PDB

Protein Data Bank

RMSD

Root-mean-square deviation

SPC

Simple point charge

Notes

Acknowledgments

We thank Hao Fan, Philippe Hünenberger, Zuo Le, Haiyan Liu, Alpesh Malde, Chris Oostenbrink, Xavier Perole, David Poger, Maria Reif, Denise Steiner, Xue Ying and Bojan Zagrovic for stimulating discussions and contributions to the force field modifications. This work was financially supported by the National Center of Competence in Research (NCCR) in Structural Biology and by grant number 200020-121913 of the Swiss National Science Foundation, by grant number 228076 of the European Research Council and by grant number DP0770375 of the Australian Research Council. All funding is gratefully acknowledged.

Supplementary material

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Copyright information

© European Biophysical Societies' Association 2011

Authors and Affiliations

  • Nathan Schmid
    • 1
  • Andreas P. Eichenberger
    • 1
  • Alexandra Choutko
    • 1
  • Sereina Riniker
    • 1
  • Moritz Winger
    • 2
  • Alan E. Mark
    • 2
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Laboratory of Physical ChemistrySwiss Federal Institute of Technology ETHZürichSwitzerland
  2. 2.School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneAustralia

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