Accurate, robust, and reliable calculations of Poisson–Boltzmann binding energies

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, ∆G_el, and binding free energy, ∆∆G_el, 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 ∆G_el obtained at the grid spacing of 1.0 Å compared to ∆G_el 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 ∆G_el calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening.