PBCAVE: Program for exact classification of the mesh points of a protein with possible internal cavities and its application to Poisson–Boltzmann equation solution

Description

The main contribution of the program is in the analytic approach to the setting of dielectric constant for all discretization points of a grid in the computational domain according to their locations with respect to the molecular surface allowing also taking into account possible cavities. Assigned values of dielectric constant are used in a solver of the linear Poisson–Boltzmann equation for a protein–water system using a finite difference method.

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