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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.
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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.
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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.
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