Definition and testing of the GROMOS force-field versions 54A7 and 54B7.
- Schmid N Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zürich, Switzerland.
- Eichenberger AP
- Choutko A
- Riniker S
- Winger M
- Mark AE
- van Gunsteren WF
- 2011-05-03
Published in:
- European biophysics journal : EBJ. - 2011
English
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.
- Language
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- English
- Open access status
- green
- Identifiers
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- DOI 10.1007/s00249-011-0700-9
- PMID 21533652
- Persistent URL
- https://folia.unifr.ch/global/documents/167844
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