|
INTERCHEM 6.1: A Comprehensive Molecular Modelling Package
by Peter Bladon and Robin Breckenridge, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland, U.K.
* * * * * * * * * * * * * * INTERCHEM is so large that it can only be shipped on a 150 Mb tape cartridge. It CAN NOT be shipped by ftp. Some of the files contained on the tape are large enough that they are stored as compressed files (.Z). Such files must simply be uncompressed using the UNIX "uncompress" command.
* * * * * * * * * * * * * * In the following description, major new facilities introduced since INTERCHEM 5.0 [QCPE Bulletin, 13, 1 (1993)] are indicated by asterisks. INTERCHEM is a molecular modelling package designed for use on Silicon Graphics Inc. workstations. It includes facilities for handling 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, which provides rapid optimisation of structures. Structure files may be read into the program in TRIPOS- SYBYL, BIOSYM-INSIGHT, Cambridge Crystallographic Data Base XR and FDAT* formats, as well as the native INTERCHEM format. A similar interface* is provided to the ab initio program GAMESS-UK. Using a modified version of MOPAC (see later entry) it is possible to create a file containing the components of the dipole moment of a structure, the moments of inertia, as well as the atom co-ordinates, all in a co-ordinate system defined by the principal axes of the structure. If this file is read by INTERCHEM, then these molecular properties can be displayed along with the structure.* The Proteins Package provides selective editing and display, highlighting of special features, display of ribbon structures and cartoons*, 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 of files in Cambridge XR and FDAT* formats and writing of files in XR format. Structures may be displayed with unit cells. A 3 x 3 x 3 nest of unit cells may be created. INTERCHEM runs on Silicon Graphics Inc. workstations having the following specifications: 1280 x 1024 display (essential), 24-bit planes for colour, 24-bit Z-buffer. It has been tested on the following types: Personal Iris 4D20, 4D35, Iris Indigo Elan, Iris Crimson Elan, Indigo-2-XZ. It also works well on Indy machines where Z-buffering is done in main memory (e.g., Indy-4000-PC). It runs under verions of 4.0.x and 5.x of the Irix operating system. Lines of Code: 73,000 FORTRAN 77 with one C-module
THREEDOM: A Program for Three-Dimensional Database Searching by Peter Bladon, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland, U.K. THREEDOM exploits the icosahedral matching algorithm^1, in a manner similar to that employed by van Geerestein and co- workers^2, for searching a database of structures held in INTERCHEM Multi-D format, for best match with a target structure. A preliminary screening (prefiltering) of the structures can be invoked to eliminate those of size and shape very different from the target. Various matching parameters can be employed based on shape and charge distribution. Structures which pass the prefilter tests are then optimally aligned with the target and stored in a named directory. Ranking the structures in order of similarity is possible on the basis of a "figure of merit" calculated by THREEDOM. INTERCHEM provides a facility for rapidly viewing the aligned structures alongside the target. Several other programs using the icosahedral matching algorithm are included with THREEDOM: PREFILTER and QUICKSCAN. With an established database, the prefilter parameters can be calculated once only using the program PREFILTER. The preliminary screening is then done with QUICKSCAN to produce an intermediate database of structures approximately the same size and shape as the target. This database is then processed by THREEDOM. COMPARISONS. This is a program which allows all structures in a series of directories to be compared and aligned with a target structure. CORRELATE. This program is directed to the pairwise comparison and alignment of all structures in one directory with all those in a second directory. The two directories may be the same, when the result is the grouping of structures in order of similarity. TESSELLATE. Direct access to the routines of the icosahedral matching algorithm is provided by this program. Starting from the co-ordinates of the icosahedron inscribed on the surface of a sphere of unit radius, the program proceeds to calculate the co-ordinates for the extra points for tessellation frequencies up to 6. The matrices for the 60 proper and 60 improper (enantiomorphic) permutations of these points are calculated. All this data is in a file and is in a form that allows simple editing to produce FORTRAN DATA statements suitable for inclusion in other programs. When distributed on tape, THREEDOM includes a data base of some 22,000 structures. (Intermediates sold by the Maybridge Chemical Company Ltd., Trevillett, Tintagel, North Cornwall PL34 0HW, U.K.)
------------------------------- References: 1. P. Bladon, J. Mol. Graphics, 7, 130 (1989). 2. V. J. van Geerestein, N. C. Perry, P.D.J. Grootenhuis, and C.A.G. Haasnoot. Tetrahedron Computer Methodology, 3, 595 (1990); N. C. Perry and V. J. van Geerestein, J. Chem. Inf. Comput. Sci., 32, 607 (1992). Lines of Code: 9200 FORTRAN 77
PRESTO: A Program for Manipulating Protein and Nucleic Acid Sequences by Peter Bladon, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland, U.K. All the functions provided in INTERCHEM for the manipulation of protein and nucleic acid sequences have been abstracted and packaged in a separate program called PRESTO. There are three main modules for (a) aligning protein sequences, (b) predicting protein secondary structure, and (c) translating nucleic acid sequences. The protein alignment facilities include a fast method of aligning many sequences, which is an adaptation of the standard Needleman and Wunch algorithm^1. Included with PRESTO is a program FINDSEQUENCE which is used to access a modified version of the PIR database (also included). FINDSEQUENCE allows the database to be searched in a variety of ways and will produce files of single sequences or multiple sequences in a format suitable for input by PRESTO. PRESTO is written for use on Silicon Graphics Inc. workstations. It requires a screen resolution of 1280 x 1024. It will work with the minimum of 8-bit colour planes and does not require Z-buffering. Hence it will work on all SGI platforms except the entry-level Indigo and Indy systems. FINDSEQUENCE does not use a graphical interface and hence is suitable for most UNIX systems.
------------------------------- Reference: 1. S. B. Needleman and C. D. Wunsch, J. Mol. Biol., 48, 443 (1970). Lines of Code: 8066 FORTRAN 77 plus one C module MOPAC: Additional Output Routines by Peter Bladon, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland, U.K. Seven additional routines ACTIV0, ACTIV1, ACTIV2, ACTIV3, ACTIV4, ACTIV5 and ACTIV6 provide output of a structure with Cartesian co-ordinates referenced to the principal axes of the molecule. In addition the components of the dipole moment in this co-ordinate system and the moments of inertia are also available. The following six data are calculated for all the heavy atoms: Self-polarisability, Electrophilic- and Nucleophilic- Frontier-Electron-Densities, Nucleophilic-, Electrophilic- and Radical-Superdelocalisabilities. All of this data is output in a file with the suffix .pro when the keyword PROPER (or PROPERTIES) is included in the command line. INTERCHEM makes use of the extra output file and can then display the dipole moment, prinipal axes, and moments of inertia along with the structure. Because modifications need to be made in the main body of MOPAC to accommodate the extra keyword and the extra subroutine calls, the distribution includes a complete source of the modified MOPAC 6.0. Lines of Code: 463 FORTRAN 77 GAMESS-UK: United Kingdom Version of the GAMESS System The INTERCHEM system has also been modified to interface with the Ab Initio system GAMESS-UK. INTERCHEM, as we deliver it, does not contain this system. However, you can discuss obtaining the system with the following person:
Dr. Paul Sherwood The price for this system is $600.00 to academics and non-profit organizations. The industrial price is $3,000.00. A License Agreement is required and blank agreements can be obtained from QCPE. |