Cavity Generation of Connolly Surfaces for Subsequent Patchwise Chemical Polarizable Continuum Model Simulation

We focus on molecular cavities which are represented in the form of Solvent Excluded Surfaces. They are featured by having smooth toroidal and spherical surface blendings between the constituting atoms. The only inputs are the nuclear coordinates, the van der Waals radii and the probe radius. From those information, our purpose is to generate a patch representation of the resulting Connolly surface.We aim at a tessellation which is conforming. The patches are represented as NURBS which are globally continuous. The resulting patches are nicely shaped and neighboring patches have comparable surface areas. An automatic way to make all normal vectors outwardly oriented is provided. We present several practical results obtained from real PDB files. We examine also the influence of different parameters to the number of patches.