A numerically stable restrained electrostatic potential charge fitting method |
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| Authors: | Juan Zeng LiLi Duan John ZH Zhang Ye Mei |
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| Institution: | 1. Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China;2. College of Physics and Electronics, Shandong Normal University, Jinan 250014, China;3. Department of Chemistry, New York University, New York, New York 10003 |
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| Abstract: | Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)‐based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER charge), and the residual part is to be determined by restrained fitting to residual ESP on grid points around the molecule. Nonuniform weighting factors as a function of the dominant charge are assigned to the atoms. Because the residual part is several folds to several orders smaller than the dominant part, the impact of ill‐conditioning is alleviated. This charge fitting method can be used in quantum mechanical/molecular mechanical (QM/MM) simulations and similar studies, where QM calculated electronic properties are frequently mapped to partial atomic charges. © 2012 Wiley Periodicals, Inc. |
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| Keywords: | restrained electrostatic potential charge fit AMBER molecular mechanics numerical stability |
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