Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field

被引:14
作者
Abella, Jayvee R. [1 ]
Cheng, Sara Y. [2 ]
Wang, Qiantao [1 ]
Yang, Wei [3 ,4 ]
Ren, Pengyu [1 ]
机构
[1] Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USA
[2] Univ Texas Austin, Dept Phys, Austin, TX 78712 USA
[3] Florida State Univ, Inst Mol Biophys, Tallahassee, FL 32306 USA
[4] Florida State Univ, Dept Chem & Biochem, Tallahassee, FL 32306 USA
基金
美国国家卫生研究院;
关键词
LIGAND-BINDING; MOLECULAR-MECHANICS; PRACTICALLY EFFICIENT; ACCURATE CALCULATION; SOLVATION; SIMULATION; SOLVENT; MODEL; DYNAMICS; EXPLICIT;
D O I
10.1021/ct500202q
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The orthogonal space random walk (OSRW) method has shown enhanced sampling efficiency in free energy calculations from previous studies. In this study, the implementation of OSRW in accordance with the polarizable AMOEBA force field in TINKER molecular modeling software package is discussed and subsequently applied to the hydration free energy calculation of 20 small organic molecules, among which IS are positively charged and five are neutral. The calculated hydration free energies of these molecules are compared with the results obtained from the Bennett acceptance ratio method using the same force field, and overall an excellent agreement is obtained. The convergence and the efficiency of the OSRW are also discussed and compared with BAR Combining enhanced sampling techniques such as OSRW with polarizable force fields is very promising for achieving both accuracy and efficiency in general free energy calculations.
引用
收藏
页码:2792 / 2801
页数:10
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