Wang Zhi-Xiang, Zhang Wei, Wu Chun, Lei Hongxing, Cieplak Piotr, Duan Yong
UC Davis Genome Center, 431 East Health Sciences Drive, University of California, Davis, California 95616-8816, USA.
J Comput Chem. 2006 Apr 30;27(6):781-90. doi: 10.1002/jcc.20386.
Based on the AMBER polarizable model (ff02), we have re-optimized the parameters related to the main-chain (Phi, Psi) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., beta, P(II), alpha(R), and alpha(L) regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the beta, P(II) and alpha(R) regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)(7)-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization.
基于AMBER可极化模型（ff02），我们通过拟合重要区域（即β、P(II)、α(R)和α(L)区域）的玻尔兹曼加权平均量子力学（QM）能量，重新优化了与主链（Phi、Psi）扭转角相关的参数。按照AMBER力场系列的命名惯例，此版本将被称为ff02pol.rl。该力场已通过与QM数据的能量比较以及水中短丙氨酸肽的副本交换分子动力学模拟进行了评估。对于Ace-Ala-Nme，β、P(II)和α(R)区域的模拟群体分别约为30%、43%和26%。对于Ace-(Ala)(7)-Nme，这三个区域的群体分别约为24%、49%和26%。两者在定性上与NMR和CD实验结论一致。与之前的力场相比，ff02pol.rl在这三个重要区域之间表现出良好的平衡。优化后的扭转参数与ff02中的参数一起，使我们能够在考虑极化的情况下对蛋白质和肽进行模拟。
