Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing

Abstract

A common problem in the calculation of electrostatic potentials with the Poisson-Boltzman equation using finite difference methods is the effect of molecular position relative to the grid. Previously a uniform charging method was shown to reduce the grid dependence substantially over the point charge model used in commercially available codes. In this article we demonstrate that smoothing the charge and dielectric values on the grid can improve the gried independence, as measured by the spread of calculated values, by another order of magnitude Calculations of Born ion solvation energies, small molecule solvation energies, the electrostatic field of superoxide dismutase, and protein-protien binding energies are used to demonstrate that this method yields the same results as the point charge model while reducing the positional errors by severak orders of magnitude. © 1997 by John Wiley & Sons, Inc.