GBr(6): a parameterization-free, accurate, analytical generalized born method.
GBr(6): a parameterization-free, accurate, analytical generalized born method.
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DOI：
10.1021/jp066284c
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发表时间：
2007-02
期刊：
影响因子：
--
通讯作者：
Harianto Tjong;Huan‐Xiang Zhou
中科院分区：
文献类型：
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作者：
Harianto Tjong;Huan‐Xiang Zhou
Poisson-Boltzmann（PB）方程被广泛用于模拟大分子的静电效应和溶剂化。广义玻恩（GB）模型已被开发来模拟PB的结果，在相当低的计算成本。在这里，我们报告了一个分析GB的方法，再现PB的结果具有高精度。分析方法建立在Gallicchio和Levy（J. Comput. Chem. 2004，25，479），并结合了Grycuk（J. Chem. Phys. 2003，119，4817）提出的对大多数GB方法中使用的库仑场近似的改进。测试PB的结果，我们的GB方法有一个平均无符号的相对误差只有0.6%的一组代表性的55种蛋白质和0.4%和0.3%，分别为折叠和未折叠构象的细胞色素b562采样在分子动力学模拟。静电溶剂化自由能对溶质和溶剂介电常数和盐浓度的依赖关系在我们的方法中得到充分考虑。
The Poisson-Boltzmann (PB) equation is widely used for modeling electrostatic effects and solvation for macromolecules. The generalized Born (GB) model has been developed to mimic PB results at substantial lower computational cost. Here, we report an analytical GB method that reproduces PB results with high accuracy. The analytical approach builds on previous work of Gallicchio and Levy (J. Comput. Chem. 2004, 25, 479), and incorporates an improvement, proposed by Grycuk (J. Chem. Phys. 2003, 119, 4817), of the Coulomb-field approximation used in most GB methods. Tested against PB results, our GB method has an average unsigned relative error of only 0.6% for a representative set of 55 proteins and of 0.4% and 0.3%, respectively, for folded and unfolded conformations of cytochrome b562 sampled in molecular dynamics simulations. The dependencies of the electrostatic solvation free energy on solute and solvent dielectric constants and on salt concentration are fully accounted for in our method.