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

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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.

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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

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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.

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Authors and Affiliations

  1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland

    Nathan Schmid, Andreas P. Eichenberger, Alexandra Choutko, Sereina Riniker & Wilfred F. van Gunsteren

  2. School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia

    Moritz Winger & Alan E. Mark

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  1. Nathan Schmid
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  2. Andreas P. Eichenberger
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  3. Alexandra Choutko
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  4. Sereina Riniker
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  5. Moritz Winger
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  6. Alan E. Mark
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  7. Wilfred F. van Gunsteren
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Correspondence to Wilfred F. van Gunsteren.

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Schmid, N., Eichenberger, A.P., Choutko, A. et al. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J 40, 843–856 (2011). https://doi.org/10.1007/s00249-011-0700-9

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  • DOI: https://doi.org/10.1007/s00249-011-0700-9

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