TY - JOUR
T1 - A test of AMBER force fields in predicting the secondary structure of Α-helical and Β-hairpin peptides
AU - Gao, Ya
AU - Zhang, Chaomin
AU - Wang, Xianwei
AU - Zhu, Tong
N1 - Publisher Copyright:
© 2017 Elsevier B.V.
PY - 2017
Y1 - 2017
N2 - 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 α-helix successfully folded to its native state, while the further folding of the β-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.
AB - 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 α-helix successfully folded to its native state, while the further folding of the β-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.
UR - https://www.scopus.com/pages/publications/85018736119
U2 - 10.1016/j.cplett.2017.04.074
DO - 10.1016/j.cplett.2017.04.074
M3 - 文章
AN - SCOPUS:85018736119
SN - 0009-2614
VL - 679
SP - 112
EP - 118
JO - Chemical Physics Letters
JF - Chemical Physics Letters
ER -