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QMAC017. MOLSVMAC: Program for the Calculation of
Molecular Volume and Surface Area
by G. M. Smith, Merck Sharp & Dohme Research
Laboratories, Rahway, New Jersey 07065
Converted by M. P. Sigalas and G. A. Katsoulos,
Laboratory of Applied Quantum Chemistry, Department of
Chemistry, Aristotle University of Thessaloniki, 540 06
Thessaloniki, Greece
This program is a conversion of the QCMP053 program for
use on the Apple Macintosh computers. The input
consists of Cartesian coordinates of atoms and the
pairs of bonded atoms. The output consists of the
total molecular volume and surface area as well as an
analysis of the participation of each individual atom
and each atom kind to the total values.
The method used to calculate the molecular volume is
based on a numerical integration using a nearly uniform
distribution of points inside a sphere. The
integration is done atom by atom using the following
procedure. A unit sphere containing 1800 points is
scaled to the size of the atom under consideration and
moved to be centered at the atomic center. Then for
every atom which overlaps the atom in question, a plane
is constructed perpendicular to the connecting line of
their centers and passing through the points of
intersection of the atomic surfaces. All points which
lie on the side of the plane away from the atomic
center are discarded. When this process is done, the
unique volume for this atom can be calculated as the
product of the number of points remaining and the
volume per point value obtained by dividing the
original atom volume by 1800. This is repeated for all
atoms in the structure, and the final sum is taken to
obtain the overall volume.
A similar method is used for the calculation of the
molecular surface area. The surface of the van der
Waals sphere of each atom considered is filled by 820
points as a set of circles separated by a constant
angle and with the points on each circle separated by
the same angle. Then, all points which lie inside of
the sphere of any other overlapping atom are discarded.
The surface for this atom can be calculated as the
product of the total surface of this atom by the number
of points remaining, divided by the total number of
points (820). This is repeated for all atoms in the
structure, and the final sum is taken to obtain the
overall surface.
In the original program the van der Waals radii of
atoms consist of internal data. In this version these
values are contained in a text file named "VDW.DAT".
Thus the user can edit this file in order to change the
radius of an atom or to add non-existing values.
Lines of Code: 1116
FORTRAN 77 (Absoft FORTRAN v.2.3)
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