Definition and testing of the GROMOS force-field versions 54A7 and 54B7

被引：1974

作者：

Schmid, Nathan ^{[1
]}

Eichenberger, Andreas P. ^{[1
]}

Choutko, Alexandra ^{[1
]}

Riniker, Sereina ^{[1
]}

Winger, Moritz ^{[2
]}

Mark, Alan E. ^{[2
]}

van Gunsteren, Wilfred F. ^{[1
]}

机构：

[1] ETH, Swiss Fed Inst Technol, Phys Chem Lab, CH-8093 Zurich, Switzerland

[2] Univ Queensland, Sch Chem & Mol Biosci, Brisbane, Qld, Australia

来源：

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS | 2011年 / 40卷 / 07期

基金：

澳大利亚研究理事会; 瑞士国家科学基金会; 欧洲研究理事会;

关键词：

GROMOS; 54A7; Force field; Secondary structure; EGG-WHITE LYSOZYME; MOLECULAR-DYNAMICS; SECONDARY STRUCTURE; NUCLEIC-ACIDS; PROTEIN; ENERGY; SIMULATION; CONSTRAINTS; 53A6; CONFORMATIONS;

D O I：

10.1007/s00249-011-0700-9

中图分类号：

Q6 [生物物理学];

学科分类号：

071011 ;

摘要：

New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new phi/psi torsional angle terms and a modification of the N-H, C=O repulsion, a new atom type for a charged -CH3 in the choline moiety is added, the Na+ and Cl- ions are modified to reproduce the free energy of hydration, and additional improper torsional angle types for free energy calculations involving a chirality change are introduced. The new helical propensity modification is tested using the benchmark proteins hen egg-white lysozyme, fox1 RNA binding domain, chorismate mutase and the GCN4-p1 peptide. The stability of the proteins is improved in comparison with the 53A6 force field, and good agreement with a range of primary experimental data is obtained.

引用

页码：843 / 856

页数：14

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