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RI-MP3 calculations of biomolecules based on the fragment molecular orbital method
Journal of Computational Chemistry ( IF 3 ) Pub Date : 2018-09-12 , DOI: 10.1002/jcc.25368
Takeshi Ishikawa 1 , Kota Sakakura 2 , Yuji Mochizuki 3, 4
Affiliation  

In this study, the third‐order Møller–Plesset perturbation (MP3) theory using the resolution of the identity (RI) approximation was combined with the fragment molecular orbital (FMO) method to efficiently calculate a high‐order electron correlation energy of biomolecular systems. We developed a new algorithm for the RI‐MP3 calculation, which can be used with the FMO scheme. After test calculations using a small molecule, the FMO‐RI‐MP3 calculations were performed for two biomolecular systems comprising a protein and a ligand. The computational cost of these calculations was only around 5 and 4 times higher than those of the FMO‐RHF calculations. The error associated with the RI approximation was around 2.0% of the third‐order correlation contribution to the total energy. However, the RI approximation error in the interaction energy between the protein and ligand molecule was insignificantly small, which reflected the negligible error in the inter fragment interaction energy. © 2018 Wiley Periodicals, Inc.

中文翻译:

基于碎片分子轨道法的生物分子RI-MP3计算

在这项研究中,使用身份(RI)近似分辨率的三阶 Møller-Plesset 微扰(MP3)理论与碎片分子轨道(FMO)方法相结合,以有效计算生物分子系统的高阶电子相关能. 我们为 RI-MP3 计算开发了一种新算法,可以与 FMO 方案一起使用。在使用小分子进行测试计算后,对包含蛋白质和配体的两个生物分子系统进行了 FMO-RI-MP3 计算。这些计算的计算成本仅比 FMO-RHF 计算高出约 5 和 4 倍。与 RI 近似相关的误差约为对总能量的三阶相关贡献的 2.0%。然而,蛋白质与配体分子之间相互作用能的RI近似误差很小,反映了片段间相互作用能的误差可以忽略不计。© 2018 Wiley Periodicals, Inc.
更新日期:2018-09-12
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