How to determine boundaries for QM/MM calculations: A guideline based on linear response function for glutathione

24th IUPAP Conference on Computational Physics

物理学;计算机科学

Yamanaka, Shusuke^1 ; Ueda, Koki^1 ; Nakata, Kazuto^2 ; Okumura, Mitsutaka^1 ; Yamaguchi, Kizashi^3 ; Nakamura, Haruki^4

Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka, Japan^1

NEC Corporation, 1-10, Nisshincho, Fuchu, 183-8501, Japan^2

TOYOTA Physical and Chemical Research Institute, Nagakute, Aichi, Japan^3

Protein Institute, Osaka University, 3-2, Yamadaoka, Suita, Osaka, Japan^4

关键词: Glutathiones;    Linear response functions;    Point charge;    Qm calculations;    QM/MM calculations;    QM/MM modeling;    Quantum mechanics/molecular mechanics;    Standard tools;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/454/1/012055/pdf
DOI  :  10.1088/1742-6596/454/1/012055

学科分类：计算机科学（综合）

来源: IOP

【 摘 要 】

Quantum mechanics/molecular mechanics (QM/MM) methods have grown to be a standard tool for chemical reactions in biological systems. Still, the remaining problem is that the MM point charges induce artificial polarizations in QM regions, spoiling the quality of the QM calculations. Thus, how to determine boundaries between QM and MM regions is an essential issue for QM/MM calculations. Recently, we proposed the use of a linear response function as an indicator to examine the validity of the replacement of QM peripheral ligands with MM point charges. In this study, we examine the glutathione molecule, for which protonation models have been proposed so far. The calculated results are discussed in relation to the QM/MM modeling of this system.