HYBRID QUANTUM MECHANICAL/MOLECULAR MECHANICAL APPROACH TO ENZYMATIC REACTIONS BY UTILIZING THE REAL-SPACE GRID TECHNIQUE
HYBRID QUANTUM MECHANICAL/MOLECULAR MECHANICAL APPROACH TO ENZYMATIC REACTIONS BY UTILIZING THE REAL-SPACE GRID TECHNIQUE
复制标题
利用实空间网格技术进行酶反应的混合量子力学/分子力学方法
DOI：
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发表时间：
2005
期刊：
影响因子：
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通讯作者：
T. Nitta
中科院分区：
文献类型：
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作者：
Takumi Hori;Hideaki Takahashi;T. Nitta
为了实现高并行效率，我们开发了一种基于实空间网格的量子/分子力学（QM/MM）程序。该方法及其并行实施的细节已经提出。我们用Kohn-Sham密度泛函理论计算了QM子系统的电子态，其中单电子波函数由分布在立方晶胞上的实空间网格表示。我们已经进行了QM/MM模拟的肽水解在人类免疫缺陷病毒1型乙酰基蛋白酶，以检查目前的QM/MM方法的可靠性。计算得到的活化能与实验结果和其他QM/MM方法的结果吻合较好。最后，我们对整个程序进行了并行化，发现网格方法在这样大规模的电子结构计算中可以提供很高的并行效率（~80%）。我们的结论是，QM/MM方法利用真实空间网格是足够的和有效的酶促反应的研究。
We have developed a novel quantum mechanical/molecular mechanical (QM/MM) code based on the real-space grids in order to realize high parallel efficiency. The details of the methodology and its parallel implementation have been presented. We have computed the electronic state of the QM subsystem using the Kohn–Sham density functional theory, where the one-electron wave functions have been expressed by the real-space grids distributed over a cubic cell. We have performed QM/MM simulations for the peptide hydrolysis in human immunodeficiency virus type-1 aspartyl protease in order to examine the reliability of the present QM/MM approach. The activation energy obtained by the present calculations shows a good agreement with the experimental results and that of the other QM/MM method. Finally, we have parallelized the whole code and found that the grid approach can afford high parallel efficiency (~80%) in such a large scale electronic structure calculation. We conclude that the QM/MM approach utilizing real-space grids is adequate and efficient for the study of the enzymatic reactions.
影响因子：
2.9
作者：
HYLAND, LJ;TOMASZEK, TA;MEEK, TD
通讯作者：
MEEK, TD