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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
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