The Silicon Graphics Teaching Laboratory
has been replaced by the
cal Information Laboratory
and this information is for historical interest only
This is a list of software available in the Silicon Graphics Teaching Laboratory. Most of the programs may be used by all
registered users in the SGTL, but some licenses require special arrangements. If in doubt,
contact Dr Jonathan Goodman. If you are reading these pages from
outside Cambridge, the descriptions of the programs may be useful to you, but you will not be able to use these
programs through the Cambridge system.
Long jobs should always be submitted to the
The commands required to run the programs are given below, in this style. For some programs, just typing the name will start the program running. Many programs, however, require a filename as well as the name, so that the program knows where to find or to store data. This is listed as program name filename. The filename can usually be any string of characters, but it is best to avoid punctuation and spaces. See an introduction to Unix for more details.
Software by Category
- Protein database (PDB) in /usr/bigdisk/brookhaven. It can also be search using quest.
Type "quest filename -db PDB". When the search is complete, type
"pdbget -l -d -f filename.pid" to copy the pdb files that have been found into your current directory.
- Cambridge Crystallographic Database
- Search this database using the program Quest. Watch the
window that you started Quest from, because messages may also appear here.
Online help is available, but only if you are logged on to one of the machines in the Silicon Graphics Teaching Laboratory. Manuals may be consulted in 340, but may not be
removed. Pluto and Gstat are also available.
- Cambridge Crystallographic Database
- Chemistry Departments
- A list of Chemistry Departments world-wide is available
- Daresbury Databases
- Databases ( REACCS; ACD; SpecInfo) are available at the Daresbury Laboratory.
- A list of Chemistry journals which provide some on-line information is available.
- IsoStar is a new program from the CCDC
to analyse the data in the crystallographic database.
- Search through unpublished crystal structures, solved in
- Chemical database program from MDL. This provides access to the chemical databases at Daresbury, and to the laboratory database of chemicals.
To run the program type: isisbase filename
To search the ISIS database at Daresbury, type: isis
- Search the Cambridge Crystallographic database
- Some of these drug-design programs have special license conditions. Consult
Jonathan Goodman (firstname.lastname@example.org) before using them
- A program to calculate, display and analyse electrostatic potentials of macromolecules
- A program to design receptors for enzyme active sites. This program is in the directory
The manual is available on-line to machines in the SGTL.
- GASP is a program for drug design
- Determines energetically favourable binding sites for ligands. This software may not be used
for collaborations with industrial companies or government departments. To use the program for
other research or teaching, contact Dr Goodman.
- A program for creating dot surfaces around molecules.
- Rapid display of Macromodel structures, publication-quality rendered pictures and analysis of normal-mode vibrations.
- chemical drawing programs (from MDL)
- A program to display 'kinemages' An example kinemage is /usr/local/examples/Demo3_1a.kin
Many kinemages are published in the journal
- A program which colours a molecular mechanics structure according
to the distribution of energy around the molecule. The results of the
calculation can be visualised using Eadfrith. Before running mmcol, it is first necessary
to run a Complete ECalc, using MacroModel. This generates a list of all the
interactions in the force field model. The program mmcol
converts this information into colours, which can be displayed using
- This is a similar program to mmcol, except that it also
expects a substructure file, and it only display the substructure.
- A program which displays peptides (PDB format) prettily
molscript filename filename
- This is a raytracing program. Used in conjunction with Mark Mackey's program
mm2pov, it can be used to
create raytraced pictures of molecules.
- Rapid display of molecules, linked to the world-wide-web
- This program visualises molecules
- A program for viewing and manipulating atomic/molecular systems from XYZ files.
Babel can be used to create XYZ files from other formats.
- A program to display and manipulate structures
- Chime is a netscape plug-in from MDL.
It allows you to manipulate molecules in a netscape window. Chime only works in 256 colour mode. If it seems not to be working, type 'netchime' instead of 'netscape'. This will start netscape in 256 colour mode.
- Maestro is a graphical user interface to both MacroModel and Jaguar
- Ab Initio and Density Functional Calculation
- MacroModel 5.5
- Molecular Mechanics Program.
- A molecular mechanics program, with an interface to semi-empirical molecular orbital calculations.
Xed/Cosmic was written by Dr J G Vinter
and supersedes the earlier program Cosmic.
- A parallel molecular dynamics simulation package
- Simulation of liquids
- A general molecular modelling program.
- A general molecular modelling program, available thanks to a donation from Glaxo.
Documentation (only available from SGTL machines)
- This program carries out calculations of various kinds for an assembly of interacting molecules.
It was written by
- This is a conformation searching program.
- Jan Florian and Arieh Warshel's program ChemSol is now available
chemsol moleculename >& moleculename.log &
Molecular Orbital Theory
- A variant of Mopac, which can calculate the effect of water on a system. Amsol 5.4 is now the default version. An earlier version can be run by typing 'amsol.OLD filename'.
Documentation and example data files are in the directory /usr/local/amsol5.4
It is essential that the input file has the extension '.dat' and that there is no file
corresponding to the name of the input file without an extension.
- Ab initio molecular orbital program
Examples of input files are in /usr/local/cadpac
- Semi empirical molecular orbital program Look in the files /info/MOPAC/mopac.help and /info/MOPAC/mopac.manual for help
- A semi empirical molecular orbital program from Oxford Molecular. Example data files are in /usr/bigdisk/om/VAMP/TESTS.
The file format is very similar to MOPAC (and the program works in a similar way), so the conversion programs for
MOPAC can also be used for VAMP. Comprehensive help files
are now available, but are only accessible from the
- cc filename
- Explorer 2.0
- SGI's AVS equivalent. A relatively simple way to make
- f77 filename
- Java is an object oriented programming language, designed to be
simple, small and portable. Netscape and some other
WWW browsers can run Java programs. Examples of Java programs are available
in the directory
/usr/local/java_demo. Online documentation
is available in the directory /usr/java/webdocs/,
including the Java Tools Reference Pages
and the Application Programming Interface documentation.
To compile a Java program, type:
- A text editor/scripting language
- Assignment of NMR Spectra by Interactive Graphics
- Acrobat Reader
- This program displays .pdf files. This is the format that some
journals (including the ACS journals) use for their supporting information.
- A program to convert between different molecular modelling
file formats. Instructions are in the file /info/babel.doc
- A program to calculate the Boltzmann factors from the .log file of a
MacroModel conformation search
- An alternative version is also available which reads the energies
from the .out file, instead of the .log file. This only works if the
energies are in the .out file (!). This will be the case if the file
was produced by a MacroModel Conformation search. The .log file may
not be available if, for example, Acca
has been used to filter the file.
- A program to convert Cadpac force constants into normal
modes that can be visualised by Eadfrith
- Bord and Bordw
- These commands create black and white backgrounds, respectively. This
is useful if photographs are to be taken of the computer screen.
(Programs written by Keith Trollope)
- Conversion Programs:
- Other programs are available
- mm2cad, mm2cos, mm2mop, mm2mopM, c2mm, mop2mm,
csd2mmod. These convert the first format (mm for MacroModel, cos for Cosmic, mop for MOPAC,
cad for Cadpac, etc) to (2) the second. To convert PDB files into
the input format for MS (connolly), use mstrans.
mop2mm has been updated by Andrew Leach.
- This is a general program to turn a MacroModel file into a Mopac file.
It takes two arguments. The first is the filename of the structure file to be converted.
The second controls what is put into the route card of the Mopac calculation. This is a
five letter code. The first three letters must be either AM1 or PM3 to decide on the
Hamiltonian. The fourth letter is either "M" for Minimise or "S" for a single
point calculation. The final letter is "Z" for an uncharged system, "N" for a system
with a charge of minus one, and "P" for a system with a charge of plus one.
- mm2mopG filename AM1MZ
- This will convert file filename
to a Mopac file using the AM1 Hamiltonian, minimising the structure, and giving no net charge
- mm2mopG filename PM3SP
- This will convert file filename
to a Mopac file using the PM3 Hamiltonian, doing a single point calculation with a charge of plus one
- This program takes a multistructure MacroModel file, converts each structure into a MOPAC input file, and minimises each one using AM1.
The program creates a new directory called mult2mop.filename and makes
a large number of files within it. The results are summarised
in the file: filename.fe.
Mult2mop only works with the old format of MacroModel data file, and
so the command m54 must be used to convert MacroModel 5.5 files
to the old format
- MacroModel 5.5 uses a compressed file format which is not understood
by all programs which were designed to be used with an earlier version
of MacroModel. This command converts the new format into the older format.
m54 inputfile outputfile
- MacroModel cannot turn united atom waters (as are often found in PDB
files) into explicit atom waters, which are required by some force fields.
This command has now been superseded by Acca
A program to display postscript files on the screen
2D and 3D graph plotting program. Type 'man gnuplot' for a brief description. Type 'help' at the gnuplot> prompt for help.
The appearance of the graphs may be altered by editing the .Xdefaults
file in your home directory. If this file does not exist (you will need
to type 'ls -a' to see it, as the file name begins with a full stop)
you can create a new one. If it does exist, new lines can be added to it.
An .Xdefaults file consisting of the two lines:
- GNU emacs is the default version.
If you are not using an X-terminal, remember to clear the DISPLAY environment variable before running
emacs (In a csh, you do this by typing 'setenv DISPLAY'). To escape from emacs, type CNTRL-x CNTRL-c.
- A simple graphical editor which runs on all the SGTL machines.
(The editor uses GL and so will not run remotely on X-terminals).
- A simple editor, which is used in the Pine mail program. This version will
not run on acal, bcal, ccal, dcal, or ecal.
- Escape from this editor by typing ZZ (to save changes) or :q! to escape without saving changes.
- This editor is still available, but you are advised to choose another.
will plot the first two lines three pixels wide, instead of just one.
This will probably look nicer.
Gzip utility - unzips, same as "gzip -d"
GNU file compressor (similar to compress)
A program to convert MOPAC force constants into normal
modes that can be visualised by Eadfrith
Octave is a program for numerical
computations, which may be compared with MATLAB.
It provides a convenient command line interface for
solving linear and nonlinear problems numerically.
Type 'help' at the octave:> prompt for on-line help.
A text editor/scripting language
Print text files to the line printer
This command will help you choose the least heavily loaded machine
for submission of batch jobs.
A calculator program for working with numbers that are square roots of rational fractions
This script, written by Mark Mackey, allows you to view MacroModel
files using Xmol, and is particularly good for viewing animations.
For an animation of the normal modes of a Lewis acid complex type
viewmmod /usr/local/examples/NMA/FMBCl01.loop and then select
Animate from Xmol's Extras menu.
Displays/converts picture files
A program to check HTML files
New Century Learning Programs, including Magnetochemistry, Ligand-Field Theory, Orbitals,
Terms and States in free-ions and linear molecules, the Prediction of d-d
Spectra, and Lecture Demonstrations. For more details, contact