title: Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.
abstract: The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf ) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson-Boltzmann equation solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software.
authors.affiliation: Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, 32306.
authors.forename: Marcia O
authors.initials: MO
authors.lastname: Fenley
authors.forename: Robert C
authors.initials: RC
authors.lastname: Harris
authors.forename: Travis
authors.initials: T
authors.lastname: Mackoy
authors.forename: Alexander H
authors.initials: AH
authors.lastname: Boschitsch
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D016008:Statistical Distributions; D013816:Thermodynamics
chemical_list: D011506:Proteins; D012997:Solvents
keywords: Poisson-Boltzmann equation; adaptive Cartesian grid; electrostatic potential; electrostatics; implicit solvent model; surface