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

• Published in: European biophysics journal Vol. 40; no. 7; pp. 843 - 856
• Main Authors: Schmid, Nathan, Eichenberger, Andreas P., Choutko, Alexandra, Riniker, Sereina, Winger, Moritz, Mark, Alan E., van Gunsteren, Wilfred F.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.07.2011; Springer Nature B.V
• Subjects: Biochemistry; Biological and Medical Physics; Biomedical and Life Sciences; Biophysics; Cell Biology; Computer Simulation; Life Sciences; Membrane Biology; Models, Molecular; Molecular biology; Nanotechnology; Neurobiology; Original Paper; Parameter estimation; Protein Structure, Secondary; Proteins; Software; Force field; Secondary structure; GROMOS; 54A7
• ISSN: 0175-7571; 1432-1017
• DOI: 10.1007/s00249-011-0700-9

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.