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

Schmid, Nathan, Eichenberger, Andreas P., Choutko, Alexandra, Riniker, Sereina, Winger, Moritz, Mark, Alan E. and van Gunsteren, Wilfred F. (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal, 40 7: 843-856. doi:10.1007/s00249-011-0700-9


Author Schmid, Nathan
Eichenberger, Andreas P.
Choutko, Alexandra
Riniker, Sereina
Winger, Moritz
Mark, Alan E.
van Gunsteren, Wilfred F.
Title Definition and testing of the GROMOS force-field versions 54A7 and 54B7
Journal name European Biophysics Journal   Check publisher's open access policy
ISSN 0175-7571
Publication date 2011-07-01
Year available 2011
Sub-type Article (original research)
DOI 10.1007/s00249-011-0700-9
Open Access Status Not yet assessed
Volume 40
Issue 7
Start page 843
End page 856
Total pages 14
Place of publication Heidelberg, Germany
Publisher Springer
Language eng
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 phi/psi 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.
Formatted 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 Clions 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.
Keyword GROMOS
54a7
Force field
Secondary structure
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID 200020-121913
228076
DP0770375
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
School of Chemistry and Molecular Biosciences
 
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