物理化学学报 >> 2003, Vol. 19 >> Issue (04): 289-292.doi: 10.3866/PKU.WHXB20030401

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一组和AMBER力场配合的普适波恩模型参数

章威;侯廷军;乔学斌;徐筱杰   

  1. 北京大学化学与分子工程学院,北京 100871
  • 收稿日期:2003-01-23 修回日期:2003-02-24 发布日期:2003-04-15
  • 通讯作者: 徐筱杰 E-mail:xiaojxu@chem.pku.edu.cn

Parameters of GB/SA Solvation Model Consistent with AMBER Force Field

Zhang Wei;Hou Ting-Jun;Qiao Xue-Bin;Xu Xiao-Jie   

  1. College of Chemistry and Molecules Engineering, Peking University, Beijing 100871
  • Received:2003-01-23 Revised:2003-02-24 Published:2003-04-15
  • Contact: Xu Xiao-Jie E-mail:xiaojxu@chem.pku.edu.cn

摘要: 提出了一套和AMBER力场相匹配的普适波恩模型参数.新的参数集包含21种原子类型的初始半径和屏蔽因子.参数通过遗传算法拟合359个小分子水合自由能的实验值得到.采用新的参数,预测了44个小分子的水合自由能,预测值和实验值能很好地吻合,而且大大优于采用Jayaram参数得到的结果.此外,采用新的参数,还预测了15个蛋白质的水合自由能,预测值和PB/SA预测得到的结果能很好地吻合.

关键词: 水合自由能, 溶剂效应, 普适波恩(GB)模型, 泊松-玻尔兹曼(PB)方程

Abstract: A new set of parameters consistent with AMBER force field for generalized Born model was proposed. The new set of parameters includes the initial radius and screen parameters for 21 atom types. The parameters were developed by fitting the experimental aqueous free energies of solvation of 359 small organic molecules using a genetic algorithm. The derived parameters were then used to predict the solvation free energy of 44 small organic molecules. The calculated results are in good agreement with the experimental values, which are much better than those using the Jayaram’s parameters. Moreover, the derived parameters were then used to predict the solvation free energy of 15 proteins, and the calculated results showed higher linear correlation with those predicted by PB/SA.

Key words: Aqueous free energy of solvation, Solvation effect, Generalized Born model, Poisson-Boltzmann equation