Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson-Boltzmann equation: Assessment of its accuracy

A full account of how to calculate the electrostatic binding energy using the finite difference solution to the linearized Poisson-Boltzmann equation (FDPB) for protein-ligand systems is described. The following tests show that the statistical and systematic errors due to discrete grid representation of molecular shape and charges amount to about 1% and 5% of calculated binding energy difference, respectively. The greater accuracy results from a three-stage error cancellation: first in ΔG_s, then ΔΔGd_s, and finally ΔΔG_ele. We conclude in this study that the intrinsic error of FDPB is mostly canceled in computing binding energy differences. Among the parameters examined, the partial charge, dielectric constant, and radius of solvent can influence the calculated results most. © 1996 by John Wiley & Sons, Inc.