GB/SA method

Zhang, X., Li, X., and Wang, R. (2009) Interpretation of the binding affinities of PTPIB inhibitors with the MM-GB/SA method and the X-score scoring function. Journal of Chemical Information and Modeling, 49, 1033-1048. 

Addition of (16.105) and (16.106) gives the GB/SA expression for AG. The GB/SA expression is readily differentiated analytically, making it easy to use in molecular-mechanics energy minimizations (one finds the geometry that minimizes the sum of the MM steric energy and AG°oiv), and molecular-dynamics and Metropolis Monte Carlo simulations with inclusion of solvent effects. The GB/SA method is available in the MacroModel program (Section 16.6). 

Qiu D, P S Shenl F P HoUinger and W C Still 1997. The GB/SA Continuum Model for Solvation. / Fast Anal5dical Method for the Calculation of Approximate Bom Radii. Journal of Physical Chcniistr 101 3005-3014. 

The generalized Born/surface area (GB/SA) model is a combination of the Born and SASA models. This method has been effective in describing the solvation of biomolecular molecules. It is incorporated in the MacroModel software package. 

GAPT (generalized atomic polar tensor) a charge calculation method GB/SA (generalized Born/surface area) method for computing solvation effects... 

GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii. 

Qiu D, Shenkin PS, Hollinger FP, Still WC (1997) The GB/SA continuum model for solvation a fast analytical method for the calculation of approximate born radii, J Phys Chem A, 101 3005-3014... 

The effect of induced dipoles in the medium adds an extra term to the molecular Hamilton operator. = -r R (16.49) where r is the dipole moment operator (i.e. the position vector). R is proportional to the molecular dipole moment, with the proportional constant depending on the radius of the originally implemented for semi-empirical methods, but has recently also been used in connection with ab initio methods." Two other widely available method, the AMl-SMx and PM3-SMX models have atomic parameters for fitting the cavity/dispersion energy (eq. (16.43)), and are specifically parameterized in connection with AMI and PM3 (Section 3.10.2). The generalized Bom model has also been used in connection with force field methods in the Generalized Bom/Surface Area (GB/SA) model. In this case the Coulomb interactions between the partial charges (eq. (2.19)) are combined... 

Reynolds, C.H. (1995). Estimating Lipophilicity Using the GB/SA Continuum Solvation Model A Direct Method for Computing Partition Coefficients. J.Chem.lnfComput.Sci., 35,738-742. 

The most rigorous dielectric continuum methods employ numerical solutions to the Poisson-Boltzmann equation [55]. As these methods are computationally quite expensive, in particular in connection with calculations of derivatives, much work has been concentrated on the development of computationally less expensive approximate continuum models of sufficient accuracy. One of the most widely used of these is the Generalized Born Solvent Accessible Surface Area (GB/SA) model developed by Still and coworkers [56,57]. The model is implemented in the MacroModel program [17,28] and parameterized for water and chloroform. It may be used in conjunction with the force fields available in MacroModel, e.g., AMBER, MM2, MM3, MMFF, OPTS. It should be noted that the original parameterization of the GB/SA model is based on the OPLS force field. 

A computationally efficient analytical method has been developed for the crucial calculation of Born radii, which is required for each atom of the solute that carries a (partial) charge, and the Gpoi term has been parameterized to fit atomic polarization energies obtained by Poisson-Boltzmann equation [57]. The GB/SA model is thus fully analytical and affords first and second derivatives allowing for solvation effects to be included in energy minimizations, molecular dynamics, etc. The Gpoi term is most important for polar molecules and describes the polarization of the solvent by the solute. As force fields in general are not polarizable, it does not account for the polarization of the solute by the solvent. This is clearly an important limitation of this type of calculations. 

Cramer, Truhlar, and co-workers developed a series of semiempirical continuum solvation models SMr, where SM stands for solvation model and x = 1,2,3,4,5 is the version number. The SMx methods are quantum-mechanical versions of Still s GB/SA... 

Using partial atomic charges in eq. (14.59) is often called the generalized Bom model, which has been used especially in connection with force field methods in the Generalized Born/Surface Area (GB/SA) model. In this case, the Coulomb interaction between the partial charges (eq. (2.20)) is combined with the Bom formula by means of a function fy depending on the intemuclear distance and Born radii for each of the two atoms,and aj. 

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