GBr(6): a parameterization-free, accurate, analytical generalized born method.
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.
Tjong
Harianto
H
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA.
Zhou
Huan-Xiang
HX
D017605:Bromine Compounds / Q000737:chemistry*; D004583:Electrons; D012492:Salts / Q000737:chemistry
D017605:Bromine Compounds; D012492:Salts