| Abstract: | A common problem in the calculation of electrostatic potentials with the Poisson-Boltzmann 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 grid 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-protein binding energies are used to demonstrate that this method yields the same results as the point charge model while reducing the positional errors by several orders of magnitude. © 1997 by John Wiley & Sons, Inc. |
