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554. GEPOL/93: Area and Volumes of Molecules
by J. L. Pascual-Ahuir and E. Silla, Departamento de Química Física, Universidad de Valencia, 46100 Burjasot (Valencia), Spain; J. Tomasi, Dipartimento di Chimica, Università de Pisa, I-56100 Pisa, Italy; and R. Bonaccorsi, Instituto di Chimica Quantistica ed Energetica Molecolare (CNR), Via Risorgimento 35, I- 56100 Pisa, Italy This program calculates the envelope surface for a molecule (as a points distribution) and computes its correspondent area and volume.As data, the coordinates of atoms, the radii assigned to them and the solvent radius (probe radius) are needed. It calculates the three kinds of envelope surfaces: The Van der Waals Molecular Surface--It is the surface resulting from a set of intersecting spheres with radii of Van der Waals, centered on selected nuclei of the molecule. The Accessible Molecular Surface--Defined by B. Lee and F. M. Richards (J. Mol. Biol., 55, 379-400 (1971)), it is the surface defined by the center of the solvent sphere (probe sphere) when it rolls around the Van der Waals surface. This program calculates this surface, adding the probe radius to every radius atom. The Molecular Surface--As defined by F. M. Richards (Ann. Rev. Biophys. Bioeng., 6, 151-176 (1977)), this surface is composed of two parts: the Contact Surface and the Reentrant Surface. Richards defines the contact surface as that part of the Van der Waals surface of each atom which is accessible to a probe sphere of a given radius. The reentrant surface is defined as the inward-facing part of the probe sphere when it is simultaneously in contact with more than one atom. The present program calculates the molecular surface by creating a set of new spheres located among the original spheres defined by the input geometry. We call this process the "smoothing" of the surface. FORTRAN 77 (VAX/VMS) Lines of Code: 910 |