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663. ARVOMOL: Surface Areas and Volumes of Molecules
by L. Fernández Pacios, Departamento de Química y
Bioquímica, ETSI Montes, Universidad Politécnica de
Madrid, 28040 Madrid, España
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. In addition, the input is so
flexible that one can easily control many options:
method of 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
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