Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptide
Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptide
复制标题
非溶剂化多肽的分子内非共价相互作用的从头算分子动力学
DOI：
10.1007/s00214-015-1799-z
复制
发表时间：
2016
期刊：
影响因子：
--
通讯作者：
Shuhua Li
中科院分区：
文献类型：
--
作者：
Lei Zhang;Tao Fang;Wei Li;Shuhua Li
基于广义能量碎裂 (GEBF) 方法的从头分子动力学 (AIMD) 用于两种非溶剂化多肽（螺旋乙酰基 (ala) 和 DNA 聚合酶亚基）的超快构象动力学。在GEBF方法中，子系统的能量和能量梯度是通过M06-2X泛函获得的，可以描述分子内非共价相互作用。结果与基于 AMBER99 和 CHARMM22 力场、半经验密度泛函紧束缚 (DFTB) 和经验色散校正 DFTB (DFTB-D) 方法的模拟获得的结果进行了比较。我们的结果表明，由于分子内非共价相互作用的描述，GEBF-M06-2X 模拟可以为两种非溶剂化多肽的构象变化提供合理的结果。 AMBER99、CHARMM22、DFTB 和 DFTB-D 模拟给出了截然不同的结果。基于GEBF-M06-2X的AIMD模拟有望应用于大型非溶剂化多肽的快速或超快构象动力学，并用于改善经验力场。
Ab inito molecular dynamics (AIMD) based on the generalized energy-based fragmentation (GEBF) approach is employed for the ultrafast conformational dynamics of two unsolvated polypeptides,-helical acetyl(ala)and a subunit of DNA polymerase. In the GEBF approach, the energies and energy gradients of subsystems are obtained with M06-2X functionals, which can describe intramolecular noncovalent interaction. The results are compared with those obtained from the simulations based on AMBER99 and CHARMM22 force fields, and semiempirical density-functional tight-binding (DFTB) and DFTB with empirical dispersion correction (DFTB-D) methods. Our results show that the GEBF-M06-2X simulations may provide reasonable results for the conformational changes of the two unsolvated polypeptides due to the description of intramolecular noncovalent interactions. The AMBER99, CHARMM22, DFTB, and DFTB-D simulations give quite different results. The GEBF-M06-2X-based AIMD simulations are expected to be applied to the fast or ultrafast conformational dynamics of large unsolvated polypeptides and to be employed for improving the empirical force fields.