Title |
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
|
---|---|
Published in |
European Biophysics Journal, April 2011
|
DOI | 10.1007/s00249-011-0700-9 |
Pubmed ID | |
Authors |
Nathan Schmid, Andreas P. Eichenberger, Alexandra Choutko, Sereina Riniker, Moritz Winger, Alan E. Mark, Wilfred F. van Gunsteren |
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. |
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Demographic breakdown
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Scientists | 1 | 100% |
Mendeley readers
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Researcher | 180 | 15% |
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Student > Doctoral Student | 82 | 7% |
Other | 161 | 14% |
Unknown | 251 | 21% |
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Physics and Astronomy | 47 | 4% |
Other | 185 | 16% |
Unknown | 307 | 26% |