Protein force-field parameters optimized with the protein data bank. II. Comparisons of force fields by folding simulations of short peptides

摘要

In Paper I of this series, the formulations of the optimization method of existing force-field parameters for protein systems have been presented. We then applied it to five sets of force-field parameters, namely, AMBER parm94, AMBER parm96, AMBER parm99, CHARMM version 22, and OPLS-AA. In order to test the validity of these force fields, the folding simulations of alpha-helical and beta-hairpin peptides have been performed with each of the original and optimized force-field parameters. We found that all five modified force-field parameters gave both alpha-helical and beta-hairpin structures more consistent with the experimental implications than the original force fields.