the goodman group
university of cambridge  


   list of software

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

Software

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 batch queue.

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


Databases

Brookhaven
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.
quest filename

Conquest
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.

Journals
A list of Chemistry journals which provide some on-line information is available.

IsoStar
IsoStar is a new program from the CCDC to analyse the data in the crystallographic database.

Labquest
Search through unpublished crystal structures, solved in Cambridge
labquest filename

ISIS/Base
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

Quest
Search the Cambridge Crystallographic database
quest filename

Drug Design

Some of these drug-design programs have special license conditions. Consult Jonathan Goodman (jmg11@cam.ac.uk) before using them

Delphi
A program to calculate, display and analyse electrostatic potentials of macromolecules
delphi

Dock
A program to design receptors for enzyme active sites. This program is in the directory /usr/bigdisk/dock. The manual is available on-line to machines in the SGTL.
/usr/bigdisk/dock/bin/dock

GASP
GASP is a program for drug design

Grid
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.
grid

MS
A program for creating dot surfaces around molecules.
connolly

Molecular Graphics

Eadfrith
Rapid display of Macromodel structures, publication-quality rendered pictures and analysis of normal-mode vibrations.
eadfrith filename

ISIS/Draw
chemical drawing programs (from MDL)
isisdraw filename

Mage
A program to display 'kinemages' An example kinemage is /usr/local/examples/Demo3_1a.kin Many kinemages are published in the journal Protein Science
mage filename

Mmcol
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 Eadfrith.
mmcol filename

Mmsbscol
This is a similar program to mmcol, except that it also expects a substructure file, and it only display the substructure.
mmsbscol filename

Molscript
A program which displays peptides (PDB format) prettily (Local documentation)
molscript filename filename

POV-Ray
This is a raytracing program. Used in conjunction with Mark Mackey's program mm2pov, it can be used to create raytraced pictures of molecules.

Rasmol
Rapid display of molecules, linked to the world-wide-web
rasmol filename

Scian
This program visualises molecules
scian

XMakemol
A program for viewing and manipulating atomic/molecular systems from XYZ files. Babel can be used to create XYZ files from other formats.
xmakemol filename

Xmol
A program to display and manipulate structures
xmol filename

Chime
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.

Molecular Modelling

Maestro
Maestro is a graphical user interface to both MacroModel and Jaguar

Jaguar
Ab Initio and Density Functional Calculation

MacroModel 5.5
Molecular Mechanics Program.
rmmod

Xed/Cosmic
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.
xed

DL_POLY
A parallel molecular dynamics simulation package

Solvation
Simulation of liquids
solvation

Cerius2
A general molecular modelling program.
cerius

Sybyl
A general molecular modelling program, available thanks to a donation from Glaxo. Documentation (only available from SGTL machines)
sybyl

Orient
This program carries out calculations of various kinds for an assembly of interacting molecules. It was written by Anthony Stone.
orient

Acca
This is a conformation searching program.

Chemsol
Jan Florian and Arieh Warshel's program ChemSol is now available
chemsol moleculename >& moleculename.log &

Molecular Orbital Theory

Amsol
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.
amsol filename

Cadpac
Ab initio molecular orbital program Examples of input files are in /usr/local/cadpac
rcadpac filename

Mopac
Semi empirical molecular orbital program Look in the files /info/MOPAC/mopac.help and /info/MOPAC/mopac.manual for help
rmopac filename

VAMP
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 SGTL.
rvamp filename

Programming

C
cc filename

Explorer 2.0
SGI's AVS equivalent. A relatively simple way to make graphical programs
explorer

Fortran77
f77 filename

Java
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:
javac filename.java

Perl
A text editor/scripting language

Tcl/Tk

Spectral Analysis

ANSIG
Assignment of NMR Spectra by Interactive Graphics (Local Documentation)
ansig controlfile.ctr

Utilities

Acrobat Reader
This program displays .pdf files. This is the format that some journals (including the ACS journals) use for their supporting information.
acroread

Babel
A program to convert between different molecular modelling file formats. Instructions are in the file /info/babel.doc
babel

Boltz
A program to calculate the Boltzmann factors from the .log file of a MacroModel conformation search
boltz

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.
boltzout

cadpacNMA
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)
bord
bordw

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.

Also:

mm2mopG
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

mult2mop
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
mult2mop filename

m54
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

mmh2o
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

Editors:
emacs
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.
emacs filename
jot
A simple graphical editor which runs on all the SGTL machines. (The editor uses GL and so will not run remotely on X-terminals).
jot filename
pico
A simple editor, which is used in the Pine mail program. This version will not run on acal, bcal, ccal, dcal, or ecal.
pico filename
vi
Escape from this editor by typing ZZ (to save changes) or :q! to escape without saving changes.
vi filename
zip
This editor is still available, but you are advised to choose another.

Ghostview
A program to display postscript files on the screen

Gnuplot
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:
gnuplot*line1Width: 3
gnuplot*line2Width: 3
will plot the first two lines three pixels wide, instead of just one. This will probably look nicer.
gnuplot

Gunzip
Gzip utility - unzips, same as "gzip -d"
gunzip filename

Gzip
GNU file compressor (similar to compress)
gzip filename

mopacNMA
A program to convert MOPAC force constants into normal modes that can be visualised by Eadfrith

Octave
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.
octave

Perl
A text editor/scripting language

Printing
Print text files to the line printer
lpr filename

rload
This command will help you choose the least heavily loaded machine for submission of batch jobs.

rrf
A calculator program for working with numbers that are square roots of rational fractions

Viewmmod
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.
viewmmod filename

XV
Displays/converts picture files
xv filename

Weblint
A program to check HTML files
weblint filename

Teaching

ncl
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 Dr Gerloch
ncl

WWW

Mosaic
Browse databases around the world (WWW)
mosaic

Netscape
Another WWW browser
netscape

Instructions for using the batch queue
Instructions for using local directories



© Goodman Group, 2005-2017; privacy; last updated May 27, 2017

department of chemistry University of Cambridge