an analytical generalized Born method with r6 integration
The GBr6 program calculates the electrostatic solvation free energy based on a Generalized Born (GB) method. The GB model provides a way to efficiently treat electrostatics of biomolecules by approximating the solvent as a continuum dielectric medium. GBr6 accurately reproduces the solvation energy calculated by the Poisson-Boltzmann (PB) equation. The formulation of GB is well known; more about this model is explained in J. Phys. Chem. B 111, 3055-3061 (2007). We have developed an accurate MM/GB method for protein binding and folding free energy calculations using GBr6 [ J. Chem. Theory Comput. 4, 1733-1744 (2008) ].
- Fast: the computational cost is much lower than that of PB solvers.
Analytical: first derivatives are available and useful for molecular dynamics (MD).
The GBr6 algorithm follows AGBNP
(developed by Emilio Gallicchio and Ronald M. Levy) which is fully analytical. However, a main difference is that AGBNP uses
traditional r4 approximation, while GBr6 uses r6 formulation as proposed
by Tomasz Grycuk in J.Chem.Phys. 119, 4817-4826 (2003).
Dependence on solute and solvent dielectric constants: follows PB (J. Chem. Phys. 125, 206101)
Salt effects: a parameter s introduced in GBr6 to account for the effects of mobile ions, mimicking the PB treatment. The functional form of the salt dependence is the same as used in GB models as implemented in the AMBER package. The Non-linear version (GBr6NL) is also available: J. Chem. Phys. 126, 195102 (2007), through fitting to the salt dependence of the solvation energy calculated by the non-linear Poisson-Boltzmann equation.
Click here to download GBr6 from sourceforge
A text documentation is available here.
Reference: J. Phys. Chem. B 111, 3055-3061 (2007).
GBr6: A Parameterization-Free, Accurate, Analytical Generalized Born Method
Authors: Harianto Tjong and Huan-Xiang Zhou
Supported in part by NIH Grant GM058187
Our group website can be found in http://www.physics.fsu.edu/~Users/Zhou/.
For questions and suggestions, please email us to address provided below. Thank you.