Influence of Grid Spacing in Poisson-Boltzmann Equation Binding Energy Estimation.

ABSTRACT: Grid-based solvers of the Poisson-Boltzmann, PB, equation are routinely used to estimate electrostatic binding, ΔΔG_el, and solvation, ΔG_el, free energies. The accuracies of such estimates are subject to grid discretization errors from the finite difference approximation to the PB equation. Here, we show that the grid discretization errors in ΔΔG_el are more significant than those in ΔG_el, and can be divided into two parts: (i) errors associated with the relative positioning of the grid and (ii) systematic errors associated with grid spacing. The systematic error in particular is significant for methods, such as the molecular mechanics PB surface area, MM-PBSA, approach that predict electrostatic binding free energies by averaging over an ensemble

SUBMITTER: Harris RC 

PROVIDER: S-EPMC3756143 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature