Effective atom volumes for implicit solvent models: Comparison between Voronoi volumes and minimum fluctuation volumes

An essential element of implicit solvent models, such as the generalized Bo rn method, is a knowledge of the volume associated with the individual atom s of the solute. Two approaches for determining atomic volumes for the gene ralized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be used with various parameter sets for protein and nucleic aci ds in the CHARMM force field are determined from a large set of known struc tures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessi bility of the structures from which they are determined. The question of wh ether to include hydrogens in the atomic representation of the solute volum e is examined. (C) 2001 John Wiley & Sons, Inc.