Generalized Born/surface area

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... 

Molecular Mechanics Poisson-Boltzmann or Generalized Born Surface Area Methods... 

The Generalized Born and Generalized Born/Surface Area Models in Molecular Mechanics... 

This combination of Equations [5] and [16] is called the Generalized Born/Surface Area model (GB/SA), and it is currently available in the Macro-ModeP computer package. The speed of the molecular mechanics calculations is not significantly decreased by comparison to the gas phase situation, making this model well suited to large systems. Moreover, the model takes account of some first-hydration-shell effects through the positive surface tension as well as the volume polarization effects. A selection of data for aqueous solution is provided later (Table 2), and the model is compared to experiment and to other models. Nonaqueous solvents have been simulated by changing the dielectric constant in the appropriate equations, 8 but to take the surface tension to be independent of solvent does not seem well justified. 

It is important to emphasize that only the solvent-accessible surface area (SASA), the generalized Born/surface area (GB/SA), and the full AMI—SM2 models purport to address local, nonelectrostatic effects. There is no a priori reason to expect the remaining purely electrostatic models to correlate closely with experiment nevertheless, it is worthwhile to examine the cross-correlations. We will highlight some of the most interesting trends. 

GB/S A Generalized-Born/Surface-Area. A method for simulating solvation implicitly, developed by W.C. Still s group at Columbia University. The solute-solvent electrostatic polarization is computed using the Generalized-Born equation. Nonpolar solvation effects such as solvent-solvent cavity formation and solute-solvent van der Waals interactions are computed using atomic solvation parameters, which are based on the solvent accessible surface area. Both water and chloroform solvation can be emulated. 

Transferrin model compounds and 44 related iron(III) crystal structures were used to modify the AMBER force field for subsequent studies of ferric transferrin. Energy minimization was conducted both in vacuo and, more interestingly, with the generalized Born/surface area (GB/SA) continuum treatment described in Section 3.7 [548]. 

A series of continuum solvation models (SMx, x = 1-5) has been developed by Truhlar and co-worker (Cramer and Truhlar [79]), based on the Generalized Born/Surface Area (GB/SA) model (Still et al. [86]). Recall that in the GB approach the molecular shape is taken into account as the solute charge is distributed over a set of atom-centered spheres. For this GB/SA model, the polarization free energy is given by... 

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. 

The change in free energy for the transfer of a solute from an aqueous to an organic solvent can be computed using a continuum solvation model (the generalized Born/surface area, GB/SA) or a quantum mechanical model such as SMI, SM2, SMS,. . . , etc., where SM denotes solvation model. These methods are less CPU intensive than the molecular dynamics or Monte Carlo approaches described below. 

Both the united atom and all-atom AMBER parameter sets have been applied in simulations of the solvation free energies for several monosaccharides. The simulations were performed with the generalized Born surface-area-dependent (GB/SA) continuum water model, and gave rise to excellent agreement with experiment for example, ACo-G cp(.a- P) =(united atom), -0.12 (all-atom), and -0.34 kcal mol (experimental), and ACD-Man/)(cr->/ ) = 0.2,5 (united atom), 0.24 (all-atom), and 0.42 kcal mol (experimental). The good agreement obtained with the continuum water simulations suggests that discrepancies between the results obtained from explicit... 

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