A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

作者：Gao, Ya^*; Zhang, Chaomin; Wang, Xianwei; Zhu, Tong^*

来源：Chemical Physics Letters, 2017, 679: 112-118.

DOI：10.1016/j.cplett.2017.04.074

• MOLECULAR-DYNAMICS SIMULATION
• GENERALIZED-ENSEMBLE SIMULATIONS
• SOLVATION FREE-ENERGIES
• SIDE-CHAIN
• IMPLICIT SOLVATION
• BACKBONE PARAMETERS
• HYDROGEN-BOND
• POLARIZATION
• PROTEINS
• MECHANICS

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.

• 出版日期2017-7-1
• 单位华东师范大学; 上海工程技术大学; 浙江工业大学