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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) |