Features of CPB : a Poisson-Boltzmann solver that uses an adaptive Cartesian grid
© 2014 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 36(2015), 4 vom: 05. Feb., Seite 235-43 |
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| Weitere Verfasser: | , , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2015
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, N.I.H., Extramural Poisson-Boltzmann equation adaptive Cartesian grid electrostatic potential electrostatics implicit solvent model surface Proteins Solvents |
| Zusammenfassung: | © 2014 Wiley Periodicals, Inc. 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 |
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| Beschreibung: | Date Completed 18.02.2016 Date Revised 08.01.2019 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.23791 |