Dear experts
Is the GBSW model available in AMBER?
GBSW = Generalized Born with a simple SWitching
From: http://www.charmm.org/documentation/c34b1/gbsw.html
The GBSW module provides the (electrostatic + nonpolar) solvation
energy and forces. A Generalized Born method is used for the
electrostatic part and the solvent-exposed surface ares for the
nonpolar part with a phenomenological surface tension coefficient.
Based on volume integration schemes used in the GBMV module [M.S. Lee,
F.R. Salabury, Jr., and C.L. Brooks III, J. Chem. Phys., 116, 10606
(2002)], we have recast the calculation of the self-electrostatic
solvation energy to utilize a simple smoothing function at the
dielectric boundary. The GBSW model is formulated in this manner to
provide consistency with the Poisson-Boltzmann (PB) theory previously
developed to yield numerically-stable electrostatic solvation forces
based on finite-difference methods [W. Im, D. Beglov, and B. Roux,
Comp. Phys. Comm., 111, 59 (1998)]. However, it is also possible to
mimic the PB results with the molecular surface by reparametrizing two
adjustable parameters, a_0 to modulate the Coulomb field term and a_1
to include a correction term beyond Coulomb field.
--
Thank you.
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Received on Thu Sep 29 2011 - 01:00:04 PDT
