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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.
* * * * * * * * * * * * * *
Editor's Note: The INTERCHEM system is a major molecular
modelling system. With the addition of the new capabilities
described in this announcement, it becomes even more
important to the modelling community. This is the sort of
system for which one might expect to pay up to $100,000 on
the commercial market. The price is only $600.00 to
academics and $3000.00 to all others. We include a blank
License Agreement with this Bulletin.
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.
* * * * * * * * * * * * * *
The INTERCHEM package, including the programs PIFF,
PROTEINS, CONVERT and the new programs PRESTO and THREEDOM
(see following entries) is available, as noted, under
license (a copy of which is included with this mailing).
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
Daresbury Laboratory
Daresbury, Warrington
Cheshire WA4 4AD
England, U.K.
FAX: 44-925-603-100
E-mail: PSH@cxa.daresbury.ac.uk
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.
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