Chemical Physics Letters, Vol.679, 112-118, 2017
A test of AMBER force fields in predicting the secondary structure of alpha-helical and beta-hairpin peptides
We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the alpha-helix successfully folded to its native state, while the further folding of the beta-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures. (C) 2017 Elsevier B.V. All rights reserved.