Availability of high-resolution X-ray crystallographic measurements of complete molecular structures provides information about the type and location of all atoms that forms the protein. In BioMOCA the protein atoms are modeled as static point charges embedded in a finite volume inaccessible to the ions and associated with a user-defined dielectric coefficient. Moreover, a number of force-field parameters are available that provide information about the charge and radii of atoms in different amino-acid groups. The conjunction of the molecular structure and force fields provide the coordinates, radii, and charge of each atom in the protein channel. BioMOCA uses such information in the standard PQR (Position-Charge-Radius) format to map the protein system onto a rectangular grid.