New Born Radii Deriving Method for Generalized Born Model.
نویسندگان
چکیده
منابع مشابه
New Born Radii Deriving Method for Generalized Born Model
Here we report a method to calculate Born radii, an important parameter used in a Generalized Born model. Traditional methods to derive Born radii are mostly based on a complicated formula, while our method is easier and more direct. Atoms are classified according to their atom type, and the Born radii of each type are obtained by fitting to experimental solvation free energy. The SMARTS langua...
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Generalized Born (GB) models provide, for many applications, an accurate and computationally facile estimate of the electrostatic contribution to aqueous solvation. The GB models involve two main types of approximations relative to the Poisson equation (PE) theory on which they are based. First, the self-energy contributions of individual atoms are estimated and expressed as "effective Born rad...
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In this paper, a new method for calculating effective atomic radii within the generalized Born (GB) model of implicit solvation is proposed, for use in computer simulations of bio-molecules. First, a new formulation for the GB radii is developed, in which smooth kernels are used to eliminate the divergence in volume integrals intrinsic in the model. Next, the Fast Fourier Transform (FFT) algori...
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ژورنال
عنوان ژورنال: ChemInform
سال: 2005
ISSN: 0931-7597,1522-2667
DOI: 10.1002/chin.200515229