Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation

被引：18

作者：

Li, Zhenyu ^{[1
]}

Yu, Haibo ^{[2
]}

Zhuang, Wei ^{[1
]}

Mukamel, Shaul ^{[1
]}

机构：

[1] Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA

[2] Univ Wisconsin, Dept Chem, Inst Theoret Chem, Madison, WI 53706 USA

来源：

CHEMICAL PHYSICS LETTERS | 2008年 / 452卷 / 1-3期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1016/j.cplett.2007.12.022

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Molecular dynamics (MD) simulations are performed for N-methylacetamide (NMA) in water at 300 K with different force fields. Compared to the three all-atom force fields (CHARMM22, AMBER03, and OPLS-AA), the united-atom force field (GROMOS96) predicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the n pi* and pi pi* transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue shifted n pi* and pi pi* energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins. (c) 2007 Elsevier B.V. All rights reserved.

引用

页码：78 / 83

页数：6

共 35 条

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