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五种典型力场对气相中不同末端氨基酸的表现
陈欣,林子敬
作者单位E-mail
陈欣 中国科学技术大学合肥微尺度物质科学国家实验室, 物理系, 合肥 230026  
林子敬 中国科学技术大学合肥微尺度物质科学国家实验室, 物理系, 合肥 230026 zjlin@ustc.edu.cn 
摘要:
选择了Amb-er99SB、CHARMM27、ENCADS、GROMOS-53A6和OPLSAA/L五种力场,并以BHandHLYP/6-311++G**优化后的气象氨基酸构型与能量作为参考标准. 研究了中性、质子化、去质子化和带帽氨基酸在不同力场下的表现. 比较了构型相对能量、顺反式结构能量差、氢键数目与强度和优化所得构型质量等代表性结果. AMBER99SB、CHARMM27和OPLSAA/L比较GROMOS53A6和ENCADS力场更为适用于气相氨基酸. 对一般性气象氨基酸和小肽分子,最推荐的力场是CHARMM27,其次为OPLSAA/L.
关键词:  氨基酸构型  相对能量  分子力场  氢键
DOI:10.1063/1674-0068/29/cjcp1507153
分类号:
基金项目:This work is supported by the National Natural Sci-ence Foundation of China (No.11374272), the National Basic Research Program of China (No.2012CB215405), and the Collaborative Innovation Center of Suzhou Nano Science and Technology.
Performances of Five Representative Force Fields on Gaseous Amino Acids with Di erent Termini
Xin Chen,Zi-jing Lin
Abstract:
There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help the selection of force fields, the performances of five repre-sentative force fields for gaseous neutral, protonated, deprotonated and capped amino acids are systematically examined and compared. The tested properties include relative conforma-tional energies, energy differences between cis and trans structures, the number and strength of predicted hydrogen bonds, and the quality of the optimized structures. The results of BHandHLYP/6-311++G(d,p) are used as the references. GROMOS53A6 and ENCADS are found to perform poorly for gaseous biomolecules, while the performance of AMBER99SB, CHARMM27 and OPLSAA/L are comparable when applicable. Considering the general availability of the force field parameters, CHARMM27 is the most recommended, followed by OPLSAA/L, for the study of biomolecules in gas phase.
Key words:  Conformation  Relative energies  Correlation coefficient  Hydrogen bond  Molecular mechanics