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首页> 外文期刊>Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena >Optimized atomic radii for protein continuum electrostatics solvation forces
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Optimized atomic radii for protein continuum electrostatics solvation forces

机译：优化的原子半径，用于蛋白质连续体静电溶剂化力

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摘要

Recently, we presented a Green's function approach for the calculation of analytic continuum electrostatic solvation forces based on numerical solutions of the finit-difference Poisson-Botzmann (FDPB) equation [Im et al., Comp. Phys. Comm. 111(1998) 59]. In this treatment the analytic forces were explicitly defined as the first derivative of the FDPB continuum electrostatic free energy with respect to the coordinates of the solute atoms. A smooth intermediate region for the solute-solvent dielectric boundary needed to be introduced to avoid abrupt discontinuous variations in the solvation free energy and forces as a function of the atomic positions. In the present paper we extend the set of optimized radii, which was previously parametrized from molecular dynamics free energy simulations of the 20 standard amino acids with explicit solvent molecules [Nina et al., J. Phys. Chem. 101 (1997) 5239], to yield accurate solvation free energy by taking the influence of the smoothed dielectric region into account.
机译：最近，我们提出了一种格林函数方法，用于基于有限差分泊松-波兹曼方程（FDPB）方程的数值解来计算分析性连续统静电溶剂化力[Im et al。，Comp。物理通讯111（1998）59]。在这种处理中，分析力明确定义为FDPB连续谱静电自由能相对于溶质原子坐标的一阶导数。需要引入用于溶质-溶剂介电边界的光滑中间区域，以避免溶剂化自由能和力随原子位置的突然突变。在本文中，我们扩展了优化半径的集合，该半径先前是通过使用显式溶剂分子对20个标准氨基酸进行的分子动力学自由能模拟来参数化的[Nina等，J。Phys。化学101（1997）5239]，以通过考虑平滑的介电区的影响来产生精确的溶剂化自由能。

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