The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)

被引:142
作者
Fedorov, DG
Kitaura, K
Li, H
Jensen, JH
Gordon, MS
机构
[1] Natl Inst Adv Ind Sci & Technol, Tsukuba, Ibaraki 3058568, Japan
[2] Iowa State Univ, Ames Lab, US DOE, Ames, IA 50011 USA
[3] Iowa State Univ, Dept Chem, Ames, IA 50011 USA
[4] Univ Iowa, Dept Chem, Iowa City, IA 52242 USA
关键词
fragment molecular orbital; FMO; polarizable continuum model; PCM; GAMESS; parallel; GDDI; protein;
D O I
10.1002/jcc.20406
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The polarizable continuum model (PCM) for the description of solvent effects is combined with the fragment molecular orbital (FMO) method at several levels of theory, using a many-body expansion of the electron density and the corresponding electrostatic potential, thereby determining solute (FMO)-solvent (PCM) interactions. The resulting method, denoted FMO/PCM, is applied to a set of model systems, including a-helices and P-strands of alanine consisting of 10, 20, and 40 residues and their mutants to charged arginine and glutamate residues. The FMO/PCM error in reproducing the PCM solvation energy for a full system is found to be below 1 kcal/mol in all cases if a two-body expansion of the electron density is used in the PCM potential calculation and two residues are assigned to each fragment. The scaling of the FMO/PCM method is demonstrated to be nearly linear at all levels for polyalanine systems. A study of the relative stabilities of alpha-helices and beta-strands is performed, and the magnitude of the contributing factors is determined. The method is applied to three proteins consisting of 20, 129, and 245 residues. and the solvation energy and computational efficiency are discussed. (c) 2006 Wiley Periodicals, Inc.
引用
收藏
页码:976 / 985
页数:10
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