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QCMP132. ARVOMOL: Surface Areas and Volumes of Molecules
by L. Fernandez Pacios, Departamento de Quimica y
Bioquimica, ETSI Montes, Universidad Politecnica de Madrid,
28040 Madrid, Spain
The purpose of the ARVOMOL program is to calculate surface
AReas and VOlumes of MOLecules by using different
computational methods. The comparison among results
obtained with distinct approaches allows much more reliable
estimations of molecular surface areas and volumes. The
main feature of the program is the capability of obtaining
for one molecule a set of results in just one run on a
Personal Computer without resorting to various programs
normally not available for PCs. In addition, the input is
so flexible that one can easily control many options:
method to use, atomic scales, output information, auxiliary
files, etc.
Following a well-established classification, three types of
molecular surfaces can be distinguished:
1. The Van der Waals molecular surface (WMS),
which is the external surface resulting from a set
of spheres centered on the atoms.
2. The accessibility molecular surface (AMS),
which is the surface accessible to the solvent
represented by a probe rigid sphere when it
rolls around the WMS.
3. The molecular surface (MS), as introduced by
Richards, which consists of two parts: the contact
surface and reentrant surface. The first is
the part of the WMS of each atom which is accessible
to the probe sphere. The reentrant surface is
the inward-facing part of the probe sphere when it is
simultaneously in contact with more than one
atom.
ARVOMOL includes the following approaches for computing
these surfaces and their corresponding volumes:
* Monte Carlo algorithm as described by Gavezzotti
* Numerical Grid method by Meyer based on his One
Element Per Point (OEPP) algorithm
* Division into cubes algorithm due to Higo and Go, as
implemented by Coser-Gaudio and Takahata
* GEPOL algorithm consisting of a tessellation method
to compute surfaces developed by Pascual-Ahuir and
Silla
* MSDOT program by Connolly based on his analytical
method to compute molecular surfaces
The Richards MS, however, can only be determined in the
GEPOL (QCPE 554) and MSDOT (QCPE 429) methods.
Lines of Code: 5280
FORTRAN 77/ PASCAL (for contours)
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