Ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

ABSTRACT: Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of

SUBMITTER: Maier JA 

PROVIDER: S-EPMC4821407 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature