Generalized Bom/Surface Area

In the majority of continuum solvation models incorporating a surface-tension approach to estimating the non-electrostatic solvation components, the index k in Eq. (11.22) runs over a list of atom types, and die user assigns the appropriate type to each atom of the solute. This is particularly straightforward for MM models, like the Generalized Bom/Surface Area (GB/SA) model (Still el al. 1990 see also Best, Merz, and Reynolds 1997), since atom types are already intrinsic to the force field approach. This same formalism has been combined with the CHARMM and Cornell et al. force fields (see Table 2.1) to define GB models for proteins and nucleic acids (Dominy and Brooks 1999 Jayaram, Sprous, and Beveridge 1998). Considering this approach applied within the QM arena, the MST-ST models of Orozco and Luque have been the most extensively developed (see, for instance, Curutchet, Orozco, and Luque 2001). 

Transferrin model compounds and 44 related iron(III) crystal structures were used to modify the AMBER force field for subsequent studies of ferric transferrin. Eneigy minimization was conducted both in vacuo and, more interestingly, with the generalized Bom/surface area (GB/SA) continuum treatment described in Chapter 2, Section 2.712201. 

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... 

Generahzed Bom model, solvation, 395 Generalized Bom/Surface Area (GB/SA)... 

To calculate free energies, one can often obtain relative SFEs with reasonable accuracy by means of implicit solvent models such as generalized Bom/ surface area (GB/SA).4 However, for calculating relative binding affinities of ligands to proteins or for determining structural and thermodynamic properties of macromolecules, it is important to use explicit solvent models to obtain accurate results, even though explicit solvent models are more expensive computationally than the implicit solvent models. 

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

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