| 五种典型力场对气相中不同末端氨基酸的表现 |
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| 引用本文： | 陈欣,林子敬.五种典型力场对气相中不同末端氨基酸的表现[J].化学物理学报,2016,29(2):179-186. |
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| 作者姓名： | 陈欣 林子敬 |
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| 作者单位： | 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,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 |
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| 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. |
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| 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.
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| 关 键 词： | 氨基酸构型 相对能量 分子力场 氢键 |
| 收稿时间： | 2015/7/15 0:00:00 |
| 修稿时间： | 9/8/2015 12:00:00 AM |
Performances of Five Representative Force Fields on Gaseous Amino Acids with Di erent Termini |
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| Xin Chen and Zi-jing Lin.Performances of Five Representative Force Fields on Gaseous Amino Acids with Di erent Termini[J].Chinese Journal of Chemical Physics,2016,29(2):179-186. |
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| Authors: | Xin Chen and Zi-jing Lin |
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| Institution: | Hefei National Laboratory for Physical Sciences at the Microscale and CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, University of Science and Technology of China, Hefei 230026, China and Hefei National Laboratory for Physical Sciences at the Microscale and CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, University of Science and Technology of China, Hefei 230026, China;Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, China |
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| 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. |
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| Keywords: | Conformation Relative energies Correlation coefficient Hydrogen bond Molecular mechanics |
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