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626. INTERCHEM: A Comprehensive Molecular Modelling System
by Peter Bladon and Robin Breckenridge, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland, UK The INTERCHEM package, including the programs PIFF, PROTEINS and CONVERT (see following entries), is available under a license (a copy of which is included with this Bulletin). INTERCHEM is a molecular modelling program which was designed for use on Silicon Graphics Inc. workstations. It includes facilities for handling both small molecules and large biomolecular structures. Building new molecules is made easy by a library of 380 pre- optimised (MOPAC) fragments. It includes an interface to the molecular mechanics program PIFF (see next entry), which provides rapid optimisation of structures. Structure files may be read into the program in SYBYL, BIOSYM, Cambridge Crystallographic Data Base XR, and native INTERCHEM formats. Structure files may be written in a format suitable for submission to the MOPAC or AMPAC programs, and the results files may be read by INTERCHEM. The Proteins Package provides selective editing and display, highlighting of special features, display of ribbon structures, investigation of homology, prediction of protein secondary structure, automatic assembly of peptides, prediction of likely important sites, etc. Output file formats include Brookhaven and the modified Brookhaven format used by DGEOM. The Crystal Structure Package allows reading and writing of files in Cambridge XR format, display of unit cells, the replication of structures necessary to fill out a 3x3x3 nest of unit cells, display of glide planes, and slicing of structures. The program also implements the fast matching algorithm1 for aligning structures. INTERCHEM runs on Silicon Graphics Inc. workstations having the following minimum specification: 1280x1024 display, 24-bit planes, 24-bit Z-buffer. It has been tested on the following types: Personal Iris 20 and 35, IRIS Indigo Elan, IRIS Crimson Elan. It is not suitable for the basic Indigo machine; in this series the minimum configuration corresponds to IRIS Indigo XS24 with hardware Z buffer. A minimum of 8 Mb of memory is needed, but 16 Mb is preferable. It runs under either 3.0x or 4.0x versions of the IRIX operating system. _________ Reference: 1. Peter Bladon, J. Mol. Graphics, 7, 130 (1989). Lines of Code: 64,000. Total disk space required 12.5 Mb FORTRAN 77 with one C-module PIFF: A Molecular Mechanics Program by Armin Widmer, Sandoz AG., Basel Switzerland PIFF (PI-SCF Force Field) is a program for molecular mechanics calculations on molecules containing delocalised pi-electrons. A combined PI-SCF-LCAO-MO and force-field method is used to compute molecular configuration and energies.1 Due to the closed-shell SCF method, PIFF is restricted to molecules with an even number of pi-electrons (including the special case of zero). Currently, PIFF is parameterised for the following atom types: C(sp3) N(sp3) O(sp3) S(bivalent) Cl H C(sp2) N(sp2) O(sp3) N(pl3) (Note that no distinction has to be made between C(sp2) and C(ar); the distinction is implicit in the method used by PIFF.) Input and output files are in SYBYL MOL file format. _________ Reference: 1. H. J. Lindner, Tetrahedron, 30, 1127-1132 (1974). Lines of Code: 7300 FORTRAN 77 PROTEINS: A Program to Access Data in the Brookhaven Databank by Peter Bladon and Robin Breckenridge, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland, UK PROTEINS is a program designed to abstract the structural information of the biomolecules held in the Brookhaven Databank and convert it into files in the standard INTERCHEM format. Protein, nucleic acid, and polysaccharide structures are addressed; both the implicit and explicit connectivities in the databank are processed into a single connectivity table. All the residue and chain information and substrate identity are retained. Files of protein sequence information can also be produced. The file-conversion facilities are supported by an index and keyword searching. As supplied, the program assumes that the Brookhaven files are held in compressed format (*****.**.Z files) and that the IRIX operating system is being used. The databank files need not be on the host computer; the program works when they are accessed over a local network. Lines of Code: 6517 FORTRAN 77 CONVERT: Structure File Format Conversion Program by Peter Bladon, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland, UK CONVERT is a program which may be used to convert a file of chemical structural data held in one format into a file using a different format. The program is easy to use, being entirely menu driven. At present, the following file formats are handled for input and output: INTERCHEM format MOPAC/AMPAC data entry and results files SYBYL 'MOL' files Cambridge Crystallographic Database 'XR' files BIOSYM Insight 'CAR' and 'MDF' files Facilities are provided for splitting SYBYL multi-MOL files into individual files of the 'MOL' type, and for converting a series of files in one format into a corresponding series in a second format. When files for MOPAC input are produced the keyword line can either be set to a default selection, or the 'SETUP' keyword (MOPAC 6.0) may be used. Lines of Code: 3572 FORTRAN 77 NOTE:There will be a two-tier pricing system used with INTERCHEM. The price to North American academic institutions will be $400.00; for other academic institutions, the cost will be $400.00 plus Air Parcel Post charges. For government, industrial and other clients the price will be $2000.00. A signed Use Agreement must accompany all orders. All academic clients should contact QCPE with regard to purchase of this system. Other clients may contact either QCPE or Professor Bladon. His FAX number is +44-41-552-5664. |