GEPOL - AN IMPROVED DESCRIPTION OF MOLECULAR-SURFACES .3. A NEW ALGORITHM FOR THE COMPUTATION OF A SOLVENT-EXCLUDING SURFACE

To understand and calculate the interactions of a solute with a solven t, a good method of computing the molecular surface is needed. Three k inds of surfaces may be used: the van der Waals Surface, the Accessibl e Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent-Excluding Surface. The new algorithm for comput ing the Solvent-Excluding Surface included in the GEPOL93 program is d escribed. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent-Excludin g Surface by filling the spaces not accessible to the solvent with a s et of new spheres. The computation is controlled by three parameters: the number of triangles per sphere, controlled by NDIV; the maximum ov erlap among the new spheres (OFAC); and the size of the smallest spher e that can be created (RMIN). The changes introduced for the computati on of the ESURF make GEPOL93 not just a new version but a new program. An estimation is made of the error in the area and volume obtained in the function of the parameters. (C) 1994 by John Wiley and Sons, Inc.