Poisson–Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ∆Gel, and binding free energy, ∆∆Gel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of ∆Gel obtained at the grid spacing of 1.0 Å compared to ∆Gel at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in ∆Gel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening.
|Number of pages||8|
|Journal||Journal of Computational Chemistry|
|State||Published - May 15 2017|
Bibliographical noteFunding Information:
D.D.N. and G.W.W. thank the Mathematical Biosciences Institute for its hospitality and support during their visit in Ohio State University, where this manuscript was finalized.
© 2017 Wiley Periodicals, Inc.
- accurate coarse grid Poisson–Boltzmann solver
- electrostatic binding free energy
- reaction field energy
ASJC Scopus subject areas
- Chemistry (all)
- Computational Mathematics