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CPB solves the nonlinear and size-modified Poisson Boltzmann equation (PBE) governing biomolecular electrostatics using an adaptive Cartesian grid (ACG). It supports non-uniform ion size models of the solvent as well as the more conventional linear and nonlinear forms of the PBE. The Cartesian grid employs an octree data structure to provide a powerful variable mesh spacing capability while simultaneously retaining a simple cell shape and a hierarchical ordering of grid elements that is intrinsically suited to multigrid. The resulting Cartesian grid-based PBE solver, CPB, solves for the electrostatic potential in and around the (bio)molecule and post-processes the solution to evaluate various energy contributions, energy derived properties such as polar solvation and binding free energies, salt sensitivities, atomic forces, bound ion numbers, and detailed visualization of surface and volume maps of the potential and derivative quantities such as ion concentrations, ionic and dielectric pressures, and induced surface charge.

CPB embodies a number of numerical and computational features that facilitate set up and operation by the user, eliminate singular behavior, promote accurate solutions especially on the surface, ensure reliable convergence behavior and allow rapid evaluation using readily accessible computer resources. Charge singularities are eliminated by solving for the reaction field potential inside the molecule and the full potential outside. A least squares reconstruction of the solution near the surface that incorporates the local continuity conditions and curvature isavailable to enhace accuracy at the interface and produce high quality maps of surface potential and induced charge. The dielectric interface is developed internally using analytical representations for the common surface definitions (van der Waals, solvent accessible, solvent excluded, and a variety of Gaussian surfaces). Solution output includes integrated data, evaluation at selected locations, 3D graphics files compatible with TecPlot, Paraview and other plotting software.