Features of CPB: A Poisson–Boltzmann solver that uses an adaptive cartesian grid |
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| Authors: | Marcia O Fenley Robert C Harris Travis Mackoy Alexander H Boschitsch |
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| Institution: | 1. Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida;2. Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas;3. Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania;4. Continuum Dynamics, Inc., Ewing, New Jersey |
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| 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 (?rf) of the electrostatic potential (?), eliminating the charge‐induced singularities in ?. CPB can also use a least‐squares reconstruction method to improve estimates of ? 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 ? 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. © 2014 Wiley Periodicals, Inc. |
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| Keywords: | Poisson– Boltzmann equation implicit solvent model electrostatics adaptive Cartesian grid surface electrostatic potential |
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