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A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model
Author(s) -
Yamagishi Junya,
Okimoto Noriaki,
Morimoto Gentaro,
Taiji Makoto
Publication year - 2014
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23728
Subject(s) - solvation , poisson–boltzmann equation , chemistry , atomic radius , dielectric , radius , implicit solvation , molecular dynamics , solvent , force field (fiction) , computational chemistry , biomolecule , thermodynamics , physics , quantum mechanics , ion , organic chemistry , computer science , biochemistry , computer security
The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N‐ and C‐terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.