Zusammenfassung
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,
$\Delta G_el$, and binding free energy, $\Delta\Delta G_el$,
is of tremendous significance to computational biophysics and biochemistry.
Recently, it has been warned in the literature (Journal of Chemical Theory and
Computation 2013, 9, 3677-3685) that the widely used grid spacing of $0.5$ \AA
$ $ produces unacceptable errors in $\Delta\Delta G_el$ estimation
with the solvent exclude surface (SES). In this work, we investigate the grid
dependence of our PB solver (MIBPB) with SESs for estimating both electrostatic
solvation free energies and electrostatic binding free energies. It is found
that the relative absolute error of $\Delta G_el$ obtained at the grid
spacing of $1.0$ \AA $ $ compared to $\Delta G_el$ at $0.2$ \AA $ $
averaged over 153 molecules is less than 0.2\%. Our results indicate that the
use of grid spacing $0.6$ \AA $ $ ensures accuracy and reliability in
$\Delta\Delta G_el$ calculation. In fact, the grid spacing of $1.1$
\AA $ $ appears to deliver adequate accuracy for high throughput screening.
Nutzer