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 Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic volumes for the generalized 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 acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessibility of the structures from which they are determined. The question of whether to include hydrogens in the atomic representation of the solute volume is examined. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1857-1879, 2001
Schaefer
Michael
M
Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 4 rue Blaise Pascal, 67000 Strasbourg, France.
Bartels
Christian
C
Leclerc
Fabrice
F
Karplus
Martin
M