Note: The documentation for programs marked with --> DOCU can be
found on line on the SGI server (fulcrum) in the directory
/e5share/softlib/docu.
A link is also provided.
Note, however, that some of the documentations consist of more than
one part and the link will only reach one of them.
The Molecular
Modeling Core, one of the
Core Facilities at Mount Sinai,
located at the
Department of Physiology & Biophysics,
offers molecular modeling
capabilities at several levels. This document gives a concise guide
to these services and describes the access to each. For actual
usage, the user is referred to the corresponding manuals (or to
people already experienced in using them).
Access is provided to several important
databases, e.g., the
Protein Data Bank (PDB) and
Genbank.
Sequence analysis and comparison tools allow the
display, editing, transforming and analysis of protein and nucleic
acid sequence data.
This includes homology searches, multiple sequence alignments, the
enumeration of the product of digestion by given enzymes and
secondary structure prediction based on empirical rules.
Analysis of molecular structure
can be performed by quantum-mechanical methods to obtain, among
others, the electronic
structure, molecular properties and a description of electrostatic
interactions. They also provide theoretical estimates of optimum
molecular geometries, energies of reactions, and are useful in
evaluating spectroscopic data.
Macromolecular associations,
e.g., protein-protein or protein-DNA interactions,
can be studied with the aid of high-resolution
graphics display systems: optimal interactions can be determined,
and conformational searches can be performed. Specialized
computational and graphical tools are also available for the
analysis of structural and energetic properties. These enable
studies of structure-function relations, e.g., from consequences of
mutations.
Molecular simulation methods provide useful tools for
description of molecular mechanisms, and are also used in
conjunction with x-ray and NMR experiments for macromolecular
structure determination.
All of the calculations can be performed either by using a
sophisticated graphical interface that allows the user to build the
system from preprogrammed building blocks, to import data from
databases, or by logging on to one of the mainframe computers and
executing the requisite programs. The resulting structures can be
viewed in 2D or 3D renderings.
The Molecular Modeling Core facility is based on a variety of
computers, some of them oriented toward graphics, others toward
number crunching. Different uses of the facility require different
levels of computer literacy. The present document collects
information on the hardware and the software that is specific to
the facility. On each individual software extensive documentationis
available that the material contained herein does not intend to
duplicate. Rather, the purpose of this document is to provide the
knowledge necessary to operate in our environment: run, compile and
write programs. To be able to do these, one has to be cognizant of
the computers, software packages and the support available.
A
companion guide
is also available providing the general
survival skills necessary to operate in a Unix or VMS environment.
The fundamentals of editing files, managing and navigating around
files, directories and file systems, use the network to access
other computers, moving files between computers and send/receive
electronic mail are provided there.
This guide is intended to be updated frequently as the
hardware configuration changes or new software is added. Any
comment, suggestion or correction would be greatly appreciated and
will be incorporated expeditiously - contact Dr. Mezei by
e-mail, telephone (X 42186) or in person (Anneberg 21-78A).
Changes, additions, tips are announced periodically in short
bulletins. Bulletins 1-44 are available in files
/e5share/softlib/docu/bulletin/bulletinxx
where xx is the year the bulletin was issued.
Bulletins starting with #45 are in html and can be found
in the directory /e5share/softlib/docu/bulletin
with names bull_NN.html where NN is the bulletin number.
This document is stored on the SGI server as
/e5share/softlib/docu/guide.html
and can be accessed from the URL
http://inka.mssm.edu.
2. COMPUTERS
The computers, also called hosts when on a network, belonging
to the facility or accessible to users of the facility are listed
in the table below, with their physical location.
Fulcrum is the file server for all the SGI's in the Annenberg
building and atlas is the file server for the
structural biology group (in the East Building).
An alias of fulcrum is inka.
inka.mssm.edu is the address of the
mail and web server of the Department of
Physiology & Biophysics.
Unless utherwise stated, logging to any of
systems will place the user into the same home directory
located on fulcrum or atlas
(see Sec. 3.6 for details).
The file servers also act as 'password server'.
This means that your password is the same on all machines
served by fulcrum and atlas, respectively.
Note, that it is important to choose a nontrivial password
(i.e., NOT your username). In particular, it should not be a
dictionary word.
Gprotein and concave
are shared-memory multiprocessor machines, mostly for number crunching.
Note that concave belongs to the
Computational Core
and gprotein is for the use of the Weinstein group.
Cyslops, cadiz, valdez, prion, fermi, fermat are newer,
tata and bonus are
older graphics workstations running the
interactive molecular graphics programs.
They are in a publicly accessible area in a room accessible all the time.
Msvax is at the department of
Biomathematical Sciences, runnig the statistical packages.
The computers york, lexington, park, madison, lenox, douglass, cpw,
columbus, amsterdam and westend (collectively referred to as the 'farm')
belong to a consortium of NIH
investigators, most of them in the Department of
Physiology & Biophysics.
They are primarily intended for parallel computations.
People belonging to the research group of the consortium members get
accounts automatically, others on a discretionary basis.
Contact Dr. Mezei for access.
The computers wall, canal, prince, spring and bleeker
belong to the Department of
Physiology & Biophysics
- they are integrated with the farm and also use york as the server.
The computers eagle1 - eagle5 are using the Alpha architecture.
Batman is a PC running Linux.
Special care must be exercised for compatibility of binary data
generated on the alpha's or on Linux systems with data generated
on the SGI's
- contact Dr. Mezei for details.
Calculations requiring more power can be performed at one of the
national supercomputer centers, like the
Cornell Theory Center.
3.
BASIC OPERATIONS.
3.1.
Obtaining accounts.
To use any of the computers in the list above it is necessary
to obtain an account first. For the Silicon Graphics machines
(except concave), contact the Physiology &
Biophysics (P&BP) system manager, Mr. Benjamin Goldsteen at Ext. 41614,
(E-mail address:
ben@inka.mssm.edu).
For an account on concave, and msvax, contact
Mr. Kevin Kelliher, Ext. 40493, Rm. 13-36
(E-mail address:
kelliher@msvax.mssm.edu).
The national supercomputer centers require a (small) grant
application that can be obtained from their web sites.
3.2.
Accessing the computers, logging in.
Each of the computers listed above can be accessed through the
Mount Sinai network.
The workstations can be used also
directly (in Rm. 21-77B) - it is a necessity for the graphics
applications. The access to the network
is described in the
companion guide.
Once logged in, application programs can be run. In some
instances, it is enough to start the program and everything will be
handled by the program itself, e.g., it will create the necessary
files and possibly ask you to provide the name of datafiles. In
most of the cases, however, one has to prepare some input files
before a program can be successfully executed. To be able to do
this, some familiarity with the operating system running on the
host is required: creating directories, copying, renaming and
moving files. A brief introduction to the Unix and VAX/VMS
operating systems and the basics of editing files is described in
the
companion guide.
There are a growing number of applications that use the so-called
X-windows
graphics interface. First, to run such
applications, you have to be logged on to an X-terminal. If that
terminal is on the machine you want to run the program you are
ready to run. If the application resides on a different system, you
have to tell that system that you actually logged on from an X
terminal - see Sec.
2.2.4.
of the companion guide.
3.3.
Creating files.
To create a new file, one has to use an editor or transfer a
file from elsewhere. Transferring files across the network can be
done with ftp, as described in Sec.
2.3.2. of the companion guide.
It is also possible to transfer files between microcomputers and
mainframes or workstations, using Kermit (described in Sec.
4.3.1. of the companion guide). In the latter case, the file was
prepared on the microcomputer (most likely with a wordprocessor)
first. An introduction to
editors is given in the companion guide.
The table below gives the name of the editors available at our
hosts.
3.4.
Printing and viewing files.
We have a script developed locally by Ben Goldsteen
called qprint is able to print files that are in a
wide variety of formats.
qprint detects the file fomats and prints them
on the output device requested.
qprint recognizes text (i.e., ASCII) files
(the simplest and the most transferable format),
postscript files (.ps), Adobe acrobat (.pdf) files, and
various graphics files: .rgb, .tiff, .jpeg and possibly .gif.
The format of the command is
qprint -to <printer name> [<format>] <filename>
where <printer name> can be
By default, images are printed at 300dpi. It is usually desirable to
print images captured from the screen at 150 dpi. The option for that
is:
qprint -to claser -dpi 150 density.rgb
To obtain a printout on the lineprinter with a header giving
the date and the filename, type
pr -f -l90 <filename> | <print command>
where <print command>
is the normal command sending the
file <filename> to the lineprinter.
We also have the public-domain program a2ps that can print a
text formatted in a variety of ways (multi column, headers,
line numbers, etc.).
Type man a2ps to obtain a list of options.
For example, a2ps myfile | qprint -to laser will give
a nice 2-column printout,
in landscape orientation, with copious labels specifying
the origin of the file and page numbers.
The view the content of a text file, either an
editor can be used
or the appropriate command of your operating system that lists the
content of a file on the terminal (see the companion guide).
Postscript (.ps) files
can be viewed by the public-domain program
ghostview (running on an
X-terminal) or by SGI's DesktopTool xpsview.
The command acrobat opens the Adobe Acrobat viewer on the
SGI graphics workstations allowing to view .pdf files.
The following options are available for viewing, editing and/or
generating printed images a graphics file:
To obtain a screen dump in RGB format
that can be further manipulated (cropped, scaled, sharpened, etc.) by these
utilities, follow the procedure described below.
3.5.
Space saving: compress, gzip and zip.
On Unix systems there are two utilities that are able to
shorten significantly the length of most files
without losing anything. Issuing the command
compress <filename> or gzip <filename>
will change the file <filename>
into a shorter file
called <filename>.Z and <filename>.gZ,
respectively.
Wild-cards can also be used in <filename>.
To reverse the process, use the commands
uncompress <filename>, and gzip -d
<filename>, respectively.
gzip is from the Open Software Foundation and is
steadily becoming the Unix standard as there are no royalties to be
paid for its use.
Files in network archives are often stored in compressed form.
Note, that there are several other compacting programs in
widespread usage, producing files with extensions such as
.zip, .zoo, .lzh.
Files with .zip extension can be created or uncompressed by the
zip and unzip commands on Concave, Fermi, and Fermat.
The others can be uncompressed on a PC - contact Dr. Mezei for
a copy of those decompression programs.
3.6.
Permanent file systems.
There are several file systems on the various machines that
contain users' home directories, scratch space, software and databases.
These are generally available on many other systems (via NFS).
The naming convention for the file systems containing user file is
/hosts/<nodename>/<filesystem type>/
where
<filesystem type> can be either
3.7.
Running number-crunching applications.
Calculations that require more than a few minutes should
be run in the background.
Furthermore, if the machine has
batch queues set up
users should send their jobs (a script file with the commands to be
executed) there and the operating system will execute them in turn
(a few at a time).
To run a job in the background, append the execution command
with & , e.g.,
calculate < input.data >& output.data &.
The command above will execute the program
calculate using the file input.data
as the standard input, put both the results and system
error messages on the file output.data
and run in the background.
This has the additional advantage that when you log off, the job
will continue to run.
To submit a script file <fn> to the queue named
<que> issue
the command qsub -q <que> <fn>. The script file's
protection has to include x, otherwise the submission will fail - type
chmod a+x <fn> to include it.
To check on the status of your job(s) issue the
command qstat [<que>]
(the <que> is optional). To delete a jobs
from a queue called <que> issue the command
qdel -k <jobid>.
3.8.
Writing programs
The writing of new programs (or modifying of existing ones)
governed by the rules of the programming language chosen and is not
described here. A corresponding compiler has to be invoked to
produce an executable code. Note that while the source code is
frequently transferable from machine to machine, the executable is
NOT. Major programming languages are reasonably well standardized,
but the compilers may have different names and options on different
operating systems. Most compilers are able to optimize at various
levels. For debugging purpose, there is the index-check option
which, when set, causes the program to perform a run-time check on
the array and string elements to see if they are within bounds. It
adds to the execution time, but it is a very important debugging
tool. Most of the compilers also have additional debugging
facilities (e.g., dbx)
that allow you to probe the status of your
variables during the run (consult the manual!). The table below
gives the minimum information necessary to compile a Fortran 77
program.
On the VAX, the FOR command has to be followed by a LINK command.
3.8.1.
Using the debugger
Once an execution terminates with a core dump the dbx
debugger can be used to examine the status of the program.
On the SGI's the command dbx <executable name>
starts the debugger, yielding a dbx> prompt.
On the alpha's you have to type dbx <executable name> core
Typing l either results in few lines of code printed, with the
line the program stopped marked, or with the message
Source not available. In the latter case, you have to keep typing
the command up until it prints the line it aborted.
If this place is inside a subroutine then
further up commands will give you the listing
of the place it was called from.
Additionally, if the program was compiled with the -g
compilation option then you can query your variables:
the command p <variable name> will print the actual value
of that variable at the time the program stopped.
Note that the -g switch prevents optimization thus it
should only be used in anticipation of the core dump.
There is an important difference between the SGI and alpha systems
in their behavior with respect to floating point exceptions.
On the SGI's the default is to continue after a floating point exception
occurred while on the alphas's the default behavior results in a core
dump. On the alpha's any of the compilation options -fpe1,
-fpe2, -fpe3, -fpe4
let the program continue (see the man pages for the difference
between them).
To abort on floating-point exception on the SGI's you have to end the
compilation command with -trapuv -lfpe and set the environmental
variable TRAP_FPE. The command
setenv TRAP_FPE "ALL=ABORT,trace(1)" will abort the
program even when an underflow occurs. More selective control can be
exercised, however, as in
setenv
TRAP_FPE "UNDERFL=ZERO;INT_OVERFL=ZERO;OVERFL=ABORT;INVALID=ABORT;DIVZERO=ABORT,
trace(1)"
Note also, that the -C compilation option will abort the program
(on the SGI's without producing a core dump)
when an index boundary is exceeded. This is quite often the prelude to
floating-point exceptions.
3.9.
Running parallel programs
There are several ways jobs can be run in parallel. They depend mainly
in the manner the data communication/sharing between processors is done.
3.9.1.
Running programs using PVM
Jobs using PVM (like Charmm)
can be executed in the following way:
IMPORTANT: NEVER do a kill -9 pid on the pid numbers of the job.
Always stop the jobs by halting the daemon with pvm.
3.9.2.
Running programs using MPI
To execute a parallel job using the MPI communication library, simply type
mpirun -np <number of CPU's> <run command>
where the <run command> is what you would type for running a single
CPU job (e.g., charmm < job.inp >& job.out &
3.10.
Tape and CD-ROM I/O
There are several tape reading and writing devices available,
as well as CD readers.
There is a 1/2" cartridge I/O,
an 8 mm tape I/O on concave,
a 4 mm tape I/O on prion, fermi, bonus
(unreliable - use it at your own risk) and tata.
Msvax can also read TK-50 and TK-70
cartridges, as well as read and write CompacTape III - contact Mr.
Kelliher.
CD readers - contact the P&BP
system manager for its use.
To access the drives on concave, you need the
computer room (21-33) key from the P&BP system manager.
Make sure that you leave it locked once you are done.
The tape devices are accessed by the tar command
(see the companion guide).
To ensure compatibility of tapes written on the different
drives, make sure that
Please note that magnetic media has an average shelf life of 5 years.
Depending on exposure to the elements, it may be longer or shorter
then the average. You should verify your old tapes at least once a year.
3.11.
SGI architectures.
The SGI machines span several different hardware architectures
Trying to run a newer executable on an older machine
results in a message about
invalid architecture. Running an older executable on a newer
machine, while possible, results in reduced performance.
IMPORTANT: It is the
users' responsibility to make sure that they run the most efficient
executable available, especially for runs taking hours or days to
complete.
3.12.
File conversions
3.12.1.
WordPerfect to html, TeX, etc. converter
On the SGI's the command wp2x command can
convert a WP 5.0 document
to an html, tex, latex, troff, gml, script document by typing
wp2x /e5share/local/lib/wp2x/ffff.cfg in.wp > out.ffff
where in.wp is the name of the WordPerfect file,
and ffff is the output format name (i.e., one of
html, tex, latex, troff,
gml, script) and out.ffff
is the converted file.
3.12.2.
HPGL to Postscript converter
To convert an HPGL (Hewlett-Packard) plot to a variety of
graphics formats (including Postscript) logon to an SGI and type
hp2xx -m <type> input.hp where
<type> can be cad (CAD compatible),
em (),
epic (TeX macros),
eps (encapsulated Postscript),
hpgl (simplified HPGL),
img (GEM's Image format),
mf (Metafont source),
pbm (Portable Bitmap),
pcl (HP-PCL Level 3),
pcx (Paintbrush format),
rgrip (Uniplex RGRIP format),
pre (Previewmode; no output),
tex (line drawing with TeX/epic macros).
3.12.3.
Postscript to Encapsulated Postscript
The command ps2eps <filename.ps> converts a regular
Postscript file to encapsulated Postcript.
3.12.4.
Postscript to PDF
The Program Adobe Distiller installed in the NT workstation
converts a Postscript file to Adobe Acrobat (.pdf) format.
4.
DATABASES
4.1.
Brookhaven Protein Database (PDB).
The Brookhaven database contains molecular structures of
macromolecules, most of them determined by X-ray diffraction
experiments. Structures obtained by NMR are also present. Besides
the structure, information about the sequence, position of crystal
waters and the method used can also be found there.
A local copy of the PDB is now kept updated weekly on concave.
The (compressed) structures are in the directory
/global/pdb/data/structures/all/pdb
/pdb.
File names containing individual structures are of the form
pdbdABd.ent where
dabd is the four-letter PDB identifier of the structure.
The latest version of the PDB is available at the Rutgers Univeristy
via the WWW at URL
http://www.rcsb.org.
It provides for searching the database and viewing the
structures, as well as downloading them.
There is also a WWW site containing a graphical annotation of the PDB
structures in a concise form (Maintained by Dr. Janet Thorton's lab)
in London, UK) called PDBsum at
http://www.biochem.ucl.ac.uk/bsm/pdbsum.
There are also several databases that
specialize to specific families of proteins. These can be conveniently
accesses from the site
http://www.blocks.fhcrc.org/~steveh/protein.html
The sequences of the proteins in the PDB have been extracted
in GCG (see Sec. 5.5.1.)
format.
It is stored on concave in /concave/pdb/seq.
4.1.
Nucleic Acid Database (NDB).
The Nucleic Acid database is maintained at Rutgers University by the
research group of Dr. Helen Berman. It is accessible
at the URL ndbserver.rutgers.edu.
4.3.
Cambridge crystallographic database.
The Cambridge database contains the crystal structures of
smaller molecules.
It is installed on Concave, together with software allowing
access to it. To start the GUI interface type
cq (make sure your DISPLAY is set!).
To access other parts of the package firs type
use csd followed by the command of your choice.
4.4.
Genbank.
Genbank contains protein and nucleic acid sequence
information.
Local copies of it can be accessed using the
GCG
(Wisconsin) package on concave. The very latest version
can be accessed via e-mail : send the word HELP to the address
retrieve@ncbi.nlm.nih.gov to obtain instructions.
BLAST searches
can also be sent by e-mail : send the word HELP to the address
retrieve@ncbi.nlm.nih.gov to obtain instructions
4.5.
EMBL.
EMBL maintains an anonymous FTP site at
ftp.embl-heidelberg.de and a
WWW site at
http://www.embl-heidelberg.de where users can
obtain molecular biology software and can access the following
databases:
Files can be downloaded by ftp or requested by e-mail thorough
their mail server. The mail server can be used from any site
(instructions can be downloaded by ftp).
4.6.
Lipid conformation
A snapshot from the lipid simulation of Venable and Pastor has
been put in the directory
/e5share/softlib/dbase/venable on the
SGI server. Follow the instructions in the README.LIPID
file found there (some files are compressed).
Parameter files of older versions of Charmm
are collected
separately from the Charmm directories and deposited into the
directory
/e5share/softlib/prog/modeling/charmm/archive/data
on the SGI server.
The Molecular Modeling Core has acquired an extensive software
library that is outlined in this section. The information here
describes only the main features and the access to the programs,
the use of each program is
described in the corresponding documentation that is available to
the users. Besides the programs already acquired, information is
kept on software available to us. This information includes a
complete catalog of the programs available at the Quantum Chemistry
Program Exchange
(QCPE)
and the program exchange maintained by the
British Science Research Council at Daresbury
CCP5).
Contact Dr. Mezei for details.
5.1.
Mathematics oriented programs.
5.1.1.
Mathematica
Mathematica is a sophisticated program to perform symbolic
mathematical operations.
Type math to start it in the command line mode or
mathematica to run it with its X-windows interface.
5.1.2.
Matlab
Matlab is an interactive software package for scientific and
engineering numeric computation, running on the graphics SGI's. It
integrates numerical analysis, matrix computation, signal
processing. It also has excellent graphics capabilities to plot
graphs in one and two dimensions. Note, that a graphics terminal is
needed to view graphics output. To run, type matlab.
If you are on a graphics terminal type terminal
and follow the directions.
Type demo for a demonstration.
5.1.3.
Numerical Recipes.
The subroutines described in the book Numerical Recipes
(together with drivers that show how to incorporate them into a
complete program) are available both in C and Fortran77. They are
stored on the SGI server, in the directories
/e5share/softlib/prog/math/nrecipes/f
/e5share/softlib/prog/math/nrecipes/c
for the Fortran and C versions, respectively.
For each program there is a subdirectory
routines and an other called
demos containing the subroutines and
corresponding demos, respectively. The demos provide a driver and
some test.
5.1.4.
IMSL.
The International Mathematical Subroutine
Library is installed on concave.
To use it, you have to execute first the command
use imsl
(you can do it in your .cshrc file).
and add $LINK_FNL to the f77 compilation command
(this will link the IMSL library to your compiled program).
5.1.5.
SAS.
The general-purpose statistical package SAS is available on
msvax. Read the files README.1ST and
SASINFO.TXT on disk$public: for its use.
5.2.
General purpose visualization programs.
5.2.1.
Gnuplot.
Gnuplot is an interactive plotting package available on the SGI's.
From a file of x,y coordinates it is able to generate
plots on a Mac or on an X-terminal (e.g., on an SGI) as well as a
postscript file. It also generates 2D and 3D plots. See Dr. Mezei
for the documentation. To execute type
gnuplot.
5.2.2.
TeX.
TeX is essentially a metalanguage (like postscript) that
produces high-quality print of mathematical 'objects'. If you have
a file written in this language, you can obtain hardcopy of it as
follows: The filename should have the extension .tex.
There are several variants, like LaTeX, REVTeX, AMSTeX.
On the SGI's, type use tex, followed by
pdftex <name> to obtain a PDF file
<name>.pdf or by
tex <name> or latex <name>
for TeX and LaTeX, respectively, to obtain the device independent
file <name>.dvi.
To obtain the postscript file, type dvips <name>
We also have a converter from WordPerfect 5.0 to LaTeX
(see Sec. 15.1.) as well as
a DOS program that converts (in a rudimentary fashion) from
WordPerfect 5.0 to LaTeX - see Dr. Mezei if interested in it.
5.3.
Electronic structure calculation.
We have currently installed the programs
Gaussian, Gamess, and Molcas for ab-initio calculations, and
the semiempirical packages Mopac and Amsol.
The SGI versions of these programs are in the directory
/e5share/softlib/prog/electron.
5.3.1.
Gaussian
The current version is Gaussian-98.
The Gaussian-94, revision E2 is still available.
On all SGI's (including the Farm) the command gaussian jobname
will submit a Gaussian job using the file jobname.g9*
as input, and jobname.g9*out as output.
To run Gaussian-94 on concave or the farm,
use gaussian94 jobname.
This command assumes that there is a directory
username (the same as your login id)
on the reserve file system of the host running the job.
The gaussian scripts sets a number of environmental
variables as follows:
On concave the variable
LD_LIBRARY_PATH has to be set to GAUSS_EXEDIR also.
Runs requiring large scratch space must be submitted with
-lf <space>mb added to the
gaussian command where
<space> is the number of megabytes of disk
space guaranteed to be available during the run (see the df
command to determine the amount of space available).
Note, that using more than one CPU (i.e., runs on the farm)
requires the line %Nproc=N
in the .g98 input file where
N is the number of processors requested.
5.3.2.
Molcas
Molcas is a direct-CI program package from B. Ross's
group in Lundt, Sweden. It is installed on
the SGI server in the directory
/e5share/softlib/prog/electron/molcas.
The executables are in the subdirectory bin
and examples can be found in the subdirectory examples.
5.3.3.
Gamess
The ab-initio package GAMESS (a descendant of HONDO)
is available on the SGI server.
To run it, type gamess <JOBNAME>.
If the 1995 version is needed add 95 to the command; the
1994 version can be accessed by adding 00.
The input data should be in a file called <JOBNAME>.inp
It is also assumed that there is a directory
username (the same as your login id)
on the reserve file system of the host running the job.
There is a directory tests in the gamess distribution directory
(/e5share/softlib/prog/electron/gamess/v99/gamess)
containing example input files (and described in the
documentation).
There are also graphics utilities available in conjunction with Gamess.
The command
5.3.4.
Mopac
---> LINK TO DOCUMENTATION
Mopac93 is in /e5share/softlib/prog/electron/mopac/v93.
Execute the shell mopac in that directory.
See also MOTECC (Sec.5.6.).
5.3.5.
Amsol
---> LINK TO DOCUMENTATION
Amsol is an extension of the semiempirical program AMPAC
to calculate aqueous solvation free energy by including the solvent
reaction field into the Hamiltonian. It is on the SGI server. To run it,
execute /e5share/softlib/prog/electron/amsol/v94/amsol.exe.
Several test input and output files are in the same directory with
extensions .dat and.out , respectively.
5.3.6.
Molden
---> LINK TO DOCUMENTATION
Molden is a package for displaying molecular density. It is tuned to
the Ab Initio packages
GAMESS* and
GAUSSIAN. It can read all the
information it needs from a GAMESS or GAUSSIAN outputfile.
Type molden on any of the graphics workstation to start the program.
5.4.
Molecular modeling.
Molecular modeling generally proceeds in three stages. The
system under study has to be 'built' in the computer in the first
stage. This may be as simple as reading in coordinates from one of
the crystallographic databases or clicking on the residue names, or
as complex as sketching the molecules with the use of the
interactive graphic systems or building it from fragments already
programmed in these programs.
The program Simulaid
has been written to facilitiate various aspects of this step.
The second stage requires a force
field, i.e., a simple mathematical model for the intermolecular
interactions. Energy minimization finds the minimum energy
structure nearest to the configuration generated in the first step.
Simulated annealing is an efficient (but not the only) way to
search for several local minima in the hope of locating the global
minimum. An equilibrium ensemble of configurations at a given
temperature can be obtained by simulation (generally molecular
dynamics, but also Monte Carlo is an option). Simulation is in
general rather time-consuming. The third stage is the analysis of
the results from the previous two. It can be as simple as the
querying of the generated structure to find out its geometrical
parameters to running specialized programs for the determination
of, say, DNA helix axis bend. Some of the 'standard' analysis
programs are described below. Other possibilities include the
animation of a molecular dynamics simulation history. Clearly, as
the questions to be asked vary from system to system,
additional programs will be needed for newly emerging questions.
Full graphics molecular modeling programs that run
interactively on the Silicon Graphics workstations are:
InsightII/Discover,
Quanta,
Sybyl,
Macromodel,
Grasp,
MSV,
Rasmol,
Molmol,
Whatif,
Moil-view, and
Midas.
These programs allow for creating and manipulating small molecules
as well as biopolymers. They provide for energy calculation,
minimization and molecular dynamics (including animation). Most of
them also handle sequence information, including various secondary
structure prediction schemes and homology searches. All of these
programs also provide a variety of analysis options. Most of these
programs can not be run remotely.
Molecular modeling programs that can be run independently
include Charmm,
Amber, Xplor,
BatchMin, Moil,
NAMD,
Boss and MMC.
The program Delphi is also
available to calculate the electrostatic solvation energy of a molecule.
Running these
programs requires the preparation
of data files and a script file containing the command that
executes the program and identifies the input and output files.
Each of these programs is reasonably well documented and examples
are provided in the manuals. Help can also be obtained from Dr.
Mezei.
Additional examples are also available from people already using these
programs. These files can be prepared and submitted remotely i.e.,
from any of the terminals in the building, or dialing up from
outside the modems attached to the terminal server or logging on to
the requisite host via Telnet from another computer.
We also have several programs that have been written for a
particular analysis task: hydrogen-bond matrix and linear distance
plot (LDP) calculation, Dials and Windows for biopolymer
characterization based on the programs Curves and Pcurves. Most of
these programs can not be run remotely.
5.4.1.
Full graphics programs
5.4.1.1.
InsightII/Discover
To start InsightII/Discover, log on to an SGI graphics workstation
and type insightII.
InsightII also provides an
interface to the Discover program package to perform minimization
and molecular dynamics.
The structures generated by Insight can be converted to Charmm,
Amber or
Moil input with the program
Intocham
(see Sec. 5.4.3.8.).
5.4.1.2.
Quanta
To use Quanta,
type quanta.
Quanta provides an interface to Charmm.
5.4.1.3.
Sybyl
To start Sybyl type sybyl on any of the SGI graphics workstations.
Sybyl also has a command-mode that allows you to run it
from non-graphics terminals.
5.4.1.4.
Macromodel
Macromodel is a molecular modeling package from Columbia
University. It allows the use of several force fields.
Minimization, molecular dynamics and Monte Carlo - molecular
dynamics combinations can be performed, either interactively or in
batch. To run it interactively (on the SGI graphics terminals)
type mmod or macromodel. The program is in the
directory
/e5share/softlib/prog/modeling/macromodel/v5.0
- the environmental variable
MMOD_ROOT should point here.
Macromodel can also be run
from a Mac running MacX.
The batch-version (called BatchMin)
executable is called bmin.
The concave-specific version of BatchMin is
/usr/local/software/bmin/bmin and on the Farm it is called
/usr/share/macromodel/bmin.
The package contains a number of utility programs as well as the program
xcluster that performs cluster analysis on distance
matrices.
5.4.1.5.
Grasp
---> LINK TO DOCUMENTATION
Grasp is a program for visualizing surface properties like
curvature, electric field. It emphasizes electrostatics and
includes a simplified version of Delphi.
To run it, type
grasp. Clicking on the right-hand mouse button pops
up the main menu.
A brief tutorial is also available.
5.4.1.6. MSV --->
LINK TO DOCUMENTATION
MSV is a surface visualization program using the molecular surface
computation package
MSMS written by Michael Sanner at Scripps.
It is faster than Grasp.
5.4.1.8. MSMS --->
LINK TO DOCUMENTATION
MSMS computes, for a given set of spheres S and a probe radius rp , the
Reduced Surface and the analytical model of the Solvent Excluded Surface
(SES). The SES can then be triangulated with a given vertex density.
The surfaces calculated by MSMS can be visualized by the program
MSV.
5.4.1.8.
Midas
Midas is an other molecular graphics program running on X-terminals
to visualize proteins, nucleic acids and small molecules and
produce publication quality figures.
It is used by Dock.
Type midas_x on one of the SGI workstations to run it.
A printed documentation is available.
5.4.1.9.
Moil-view
--> LINK TO DOCUMENTATION
Moil-view is written by Carlos Simmerling. It was designed to work
primarily with
Moil and Amber
but Charmm and PDB input
is also supported.
Type Moil-view on any of the newer graphics workstation.
5.4.1.10.
Rasmol
Rasmol is a public-domain
molecular graphics program running on X-terminals
to visualize proteins, nucleic acids and small molecules and
produce publication quality figures. Type
rasmol on an X-terminal
logged on to gene to run it. Help is available at the
command line.
Molmol is a full graphich program from the Wutrich Laboratory
In Zurich.
Detailed information can be found at the URL
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/.
Besides tha documentiation, there is an on-line
tutorial.
5.4.1.12.
Whatif
Whatif is a collection of modeling and sequence analysis programs
with a graphics interface.
It has been installed on the SGI's.
It starts by typing whatif.
There is a printed manual and there are tutorials.
5.4.1.13. Molscript
--->
LINK TO DOCUMENTATION
Molscript, written by Per Kraulis,
creates schematic or detailed molecular graphics images
from molecular coordinates, usually, mostly for protein structures.
Its use requires a prior use global command.
The command molauto pdb1crn.ent > molscr.inp
followed by molscript -ps <. molscr.inp > molscr.ps
produces a Postscript file molscr.ps generated with the
default options.
5.4.2.
Batch oriented molecular modeling programs
5.4.2.1.
Charmm --->
LINK TO DOCUMENTATION
V24 text
V26 HTML
DOCU (V27 text)
Charmm is the most widely used modeling program at the Core
and several versions of it are available. The executables are in
/e5share/softlib/prog/modeling/charmm/execs for
bonus and tata and in
/usr/local/software/charmm/execs for concave and
prion and in /usr/share/charmm on the farm.
While executables in /e5share do run on concave, they run
significantly slower, so make sure you are using the
right directory. The various executables are listed below.
See Sec. 3.9.1 for instructions how to run
parallel jobs under PVM.
The toppar directory of the older versions have been placed
into
/e5share/softlib/prog/modeling/charmm/archive/data/toppar_22
and
/e5share/softlib/prog/modeling/charmm/archive/data/toppar_23
5.4.2.2.
Amber
Version 4.0 of the Amber package
is on the SGI server in the directory
/e5share/softlib/prog/modeling/amber/v4.0N .
Version 4.1 and 5.0 (incorporating the newer analysis program
Carnal) is on the SGI server in the directory
/e5share/softlib/prog/modeling/amber/v4.1
and
/e5share/softlib/prog/modeling/amber/v5.0, respectively,
for runs on bonus and tata.
For runs on concave or prion there is a
single-processor version in /usr/local/software/amber
and a multi-processor version in /usr/local/software/amberp.
Amber 5.1 is also available on the farm in the directory
/usr/share/amber.
Versions starting with 4.1 contain an interactive interface to generate the
Amber input files called Leap.
To run the interface, first source the file
leap/leapSetup.csh in the Amber 4.1 directory. On a vt100
terminal type tleap
to start it. On an X-terminal type xleap
(you have to execute the requisite setenv DISPLAY
command as well).
5.4.2.3.
UHBD
---> LINK TO DOCUMENTATION
--> DOCU
The command uhbd starts the
University
of Houston Brownian Dysnamics program.
Among others, it performs Brownian dynamics simulations and
solves the Poisson-Boltzmann equation.
5.4.2.4.
Xplor
Xplor is the molecular modeling package developed by Axel Brunger's group
at Yale.
Type xplor at any of the SGI's to run it.
Tutorials are available in the subdirectories of the directory
/e5share/softlib/prog/modeling/xplor/tutorial.
5.4.2.5.
Moil
---> LINK TO DOCUMENTATION
Moil, the molecular dynamics package developed by Ron Elber's
group, is installed on the SGI server. Its unique feature is Elber's
Locally Enhanced Sampling (LES) technique designed to overcome the
multiple minima problem. The latest version is in the directory
/e5share/softlib/prog/modeling/moil/v96/sgi/moil.export. The
executable programs are in the subdirectory
exe. The
documentation and a tutorial are only available in an earlier
version:
/e5share/softlib/prog/modeling/moil/v94 in the
subdirectory moil.doc, examples are in the subdirectory of
moil.tests6.
An SGI viewing program, moil-view is also available in the
directory /e5share/softlib/prog/modeling/moil/v93
/moil-view.0005.
The documentation is in doc.0005
and the executable is exe/moil-view/exe.
5.4.2.6.
NAMD ---> LINK TO DOCUMENTATION
NAMD is a fast molecular dynamics program from the
Theoretical Biophysics Group at
the University of Illinois and Beckman Institut
5.4.2.7.
MMC ---> LINK TO DOCUMENTATION
MMC is a Metropolis Monte Carlo program to model the solvation
in the canonical or isobaric or grand-canonical ensemble or to model
the transformation of one
solute into another. Several novel free-energy methodologies are
implemented. It can also perform the analysis of the simulation
history by partitioning the solvents by their proximity to the
various functional groups of the solute.
The input for such analysis can also be a
Charmm or Amber
trajectory file.
See Dr. Mezei for the latest version of the program.
5.4.2.8.
Delphi
---> LINK TO DOCUMENTATION
Delphi solves the linearized Poisson-Boltzmann equation for
irregular shaped charged systems immersed in a dielectric. Both the
charges and the dielectric constants at the various locations of
the system are specified by the user. The latest version of Delphi
has been installed on the SGI server in
/e5share/softlib/prog/modeling/delphi.
The executable is in the subdirectory
export/yas/qdiffyas2. Example parameter file is in
export/pti.
5.4.2.9.
Maxwell
---> LINK TO DOCUMENTATION
The program package Maxwell (QCPE #637) calculates
electrostatic interactions of either a finite set or of a crystal
of polarizable molecules. The molecular charge distribution are
characterized by a multipolar expansion in the form of general
directional derivatives, based on the formalism of Maxwell.
The package can also
obtain multipole moments of arbitrary order from
a one-determinental Gaussian wave function. For crystals the
permanent multipole contribution is calculated with Campbell's
generalization of the Ewald method to lattices of multipoles of
arbitrary order. Calculation of energy contributions in the form of
inverse distance power terms is also provided for. See Dr. Mezei
for references or the programs.
5.4.2.10.
Qpack
---> LINK TO DOCUMENTATION
The program package Qpack from UCFS (obtained for us by Dr.
Osman) has been installed on the SGI server in the directory
/e5share/softlib/prog/modeling
/qpack. It calculates both a 'contact list' and a
residue-based energy for a protein in a given
conformation to quantify the packing efficiency.
5.4.2.11.
Polyrate
---> LINK TO DOCUMENTATION
Polyrate is a program for calculation of reaction rates based
on information about the intermolecular potential surface using
transition state theory. Its use requires that you provide the
energy calculation routines. The programs can be found on the SGI server
in /e5share/softlib/prog/modeling/polyrate.
5.4.2.12.
A. Rashin's solvation program
A program calculating hydration enthalpy of a polar or ionic
molecules, based on a continuum solvation model of Alex
Rashin (and written by him), is on the SGI server, in the directory
/e5share/softlib/prog/misc/csolvation. The directory
contains the documentation and sample scripts, as well as the
executables and data files.
5.4.2.13.
Jumna and Ligand
Jumna can build, manipulate and energy minimize fragments of
DNA or RNA based on the helicoidal parameter set defined by Lavery
and coworkers. A variety of constraints can be imposed. Input data
can be prepared by the program Curves
(see 5.4.3.3.) or the companion program Nchem.
Ligand can energy minimize a molecule or
a molecular complex. Jumna, Ligand and Nchem are installed on gene
as /e5share/softlib/prog/modeling
/curves_plus/jum8/Jum8_s,
/e5share/softlib/prog/modeling/curves_plus/lig4/Lig4_i,
/e5share/softlib/prog/modeling/curves_plus/nchem/Nchem_i,
respectively. The commands jumna, ligand and nchem run them.
5.4.2.14.
Flexsrch
---> LINK TO DOCUMENTATION
The program package Flexsrch that performs automated docking
of a ligand including the exploration of the conformational space
(working in tandem with Amber 4) has been
installed on the SGI server.
It has been written by Andrew Leach and is described in J.
Mol.Bio., Vol. 235 p
345 (1994). The executables and the data files are
in the Amber 4.0 directory
(see Sec. 5.4.2.3 above) in the
subdirectory leach.dock.
5.4.2.15.
Congen
Congen is written by R.E. Bruccoleri to perform an exhaustive
conformational search. The program is a descendant of
Charmm.
It is in the directory
/e5share/softlib/prog/misc/congen
(with documentation and test), and the executable is called
congen.
The executable for the concave architecture is
/usr/local/software/congen.
5.4.2.16.
Modeller
--->
LINK TO DOCUMENTATION
Modeller is a program for protein modeling with spatial
restraints written by Andrej Sali. It is most frequently used for
homology or comparative modeling.
For details see their
home page.
Type modeller <command file> to run it.
Test cases are in the directory
/e5share/softlib/prog/modeling/modeller/modeller4/scripts
on the SGI server.
The command files have the extension <top>.
A printed documentation is available.
5.4.2.17.
Plotcorr
---> LINK TO DOCUMENTATION
Interactive representation of predicted residue contacts from correlated
mutations and other protein structure prediction data.
The program takes as only input a multiple sequence alignment in .hssp format
This files are generated and used by the PHD sever at the
EMBL.
Clustal can also be used to convert from other formats.
As optional input the program can read the secondary structure and accesibility
from the file that the PHD server returns as an accesibility and secondary
structure prediction query.
To run it (on any SGI graphics workstation), type
plotcorr <hssp_file> [<PHDfile>]
5.4.2.18.
Boss
Boss is the Monte Carlo program developed by W.L. Jorgensen.
It is on the SGI server in /e5share/softlib/prog/modeling/boss.
The executable is called BOSS34 and a sample command file
uboptcmd is also available there.
The concave-specific executable is
/usr/local/software/boss.
5.4.3.
Structure and simulation analysis programs
5.4.3.1.
ldp
Calculates and plots a linear distance plot on the HP plotter.
Execute interactively from any graphics terminal
running IRIX 5.3 or lower
/e5share/softlib/prog/misc/alanexe/ldp
and answer the questions.
5.4.3.2.
hb
Calculates and plots hydrogen-bond distance matrix and linear
distance plot (written by Alan Factor). The programs are on the
SGI server in the directory
/e5share/softlib/prog/misc/alanexe. The
program runs on phage: hb2p. It has to be
executed interactively to obtain the plots.
5.4.3.3.
Curves, Pcurves
Curves calculates the helicoidal parameters of a nucleic acid
as defined by Lavery and coworkers. Pcurves contains the
corresponding generalization to polypeptide chains. Both are
accessible through the program Dials and Windows. Curves 4.1 can
also be run independently of Dials and Windows on the SGI server. Type
curves to run it.
5.4.3.4.
Dials and Windows
Provides a compact display of the output from Curves and
Pcurves. To be able to run it (on the graphics workstations or on
the SGI's), put
/e5share/softlib/prog/modeling/dials/exe
into the PATH statement of your .cshrc file. There are sample
inputfiles and scripts in the directories
/e5share/softlib/prog/modeling/dials/iris/examples.
You can copy
any of these files to your directory, modify the .com file
as required and source it, followed by the command dials to run.
The graphics output will appear as postscript files and - if run on
an SGI workstation - on the screen.
5.4.3.5.
Brookhaven
PDB analysis programs (Procheck)
-->
LINK TO DOCUMENTATION
The Brookhaven
PDB has developed a number of Fortran programs
facilitating the analysis of the structures. These programs are
described in the PDB Newsletter - see Dr. Mezei. They can be found
in /e5share/softlib/prog/modeling/procheck/EXE.
on the SGI server. The command
procheck input.pdb resolution
will run the whole suit and the command
proplot input.pdb resolution runs the program pplot where
input.pdb is the input PDB filename and resolution is the
resolution of the structure (in A).
5.4.3.6.
Mepsi
---> LINK TO DOCUMENTATION
Mepsi, written by Ann Richards, calculates a molecular
similarity index based on the comparison of the respective
electrostatic potential maps. It is installed on the SGI server in the
directory /e5share/softlib/prog/modeling/mepsi
containing sample files needed to run the program.
To execute it type mepsi.
5.4.3.7.
Simloc
---> LINK TO DOCUMENTATION
Simloc, written by Dr. Mezei, takes as input the coordinates
(in PDB, Charmm or Insight format) of two molecules (or two
conformations of a molecule) and detects local similarities, i.e.,
generates substructures with low RMS. The substructures found
depend on a threshold parameter RMSmax, the smaller
RMSmax is, the
smaller in general will the substructure RMS's be. The substructure
RMS values are not limited by RMSmax, though.
To execute the program, type simloc on the SGI's and answer
the quiz.
5.4.3.8.
DSSP
---> LINK TO DOCUMENTATION
DSSP is the program used to create the
IDITIS database. It
reads in a protein structure in PDB format and
analyzes it for structural motifs.
Type (on the SGI's)
dssp <input file name> <output filename>
to run it.
5.4.3.9.
Gepol
---> LINK TO DOCUMENTATION
Gepol is the program of Juan Luis Pascal calculating
molecular surfaces defined in three different ways. The latest
version is in the directory
/e5share/softlib/prog/modeling/gepol. The executable
is gepol93.
Type gepol to run it. The directory also contains older
versions and examples.
5.4.3.10.
Simulaid
---> LINK TO DOCUMENTATION
Simulaid, written by Dr. Mezei, is a collection of utilities
helping the setup and analysis of a simulation. It can
perform the following operations:
Type simulaid to run the program and answer the quizzes.
5.4.3.11.
Intocham
---> LINK TO DOCUMENTATION
Intocham converts a .car file generated by
Insight into a
complete (including topology files) input for either Charmm or
Amber or
Moil. It can also convert the
Charmm structure back to
Insight. To run it, type intocham on
the SGI's and answer
the quizzes. Contact Dr. Mezei if problems arise - there can be a
number of ambiguities in the type conversions.
5.4.3.12.
Babel
Babel is a coordinate file conversion program, able to
interconvert among a number of formats used by popular modeling and
ab initio programs.
It runs only under IRIX 5.3 or lower (on bonus or tata)
Type babel -m to
be presented with the menu and answer the quiz.
5.4.3.13.
Ligplot, Hbplus
---> LINK TO DOCUMENTATION
The program Ligplot (from J. Thornton's lab) produces a nice
schematic drawing of the environment of a ligand (based on a given
structure) marking hydrogen bonds and hydrophobic contacts has been
installed on Gene. The hydrogen bonds are established from the
program Hbplus, also installed and called automatically by
Ligplot.
To run it, type
source /e5share/softlib/prog/modeling/ligplot/cshrc
followed by
ligplot <PDB file name>
startres endres chainID -h
where the ligand stretches from residue startres
and ends at residue number endres
and its chain identifier is chainID.
Adding the -h will have the program prompt you for a plot
title.
The resulting (Postscript) plot will be in a file called
ligplot.ps.
Hbplus can also be run independently and its parameters can
also be changed.
5.4.3.14.
Dock
Dock is a collection of program that allows the search of a database to find
matches with a target structure.
It has been installed on the SGI server in
/e5share/softlib/prog/modeling/dock.
Examples are provided in the subdirectory examples
and there is a file file.list describing the content of each file
in the dock directory tree.
A printed documentation is also available.
5.4.3.15.
Rutgers Nucleic Acid Analysis Programs
This is a DNA analysis package,
written in the laboratory of Wilma Olson at Rutgers
by Marla S. Babcock.
It has been documented in a paper
(Babcock, M.S., Pednault, E.P.D, and Olson, W.K., "Nucleic Acid
Structure Analysis: A Users Guide to a Collection of New
Analysis Programs," Journal of Biomolecular Structure and
Dynamics, Vol. 11, No. 3, pp 597-628, 1993.)
Dr. Mezei has a copy.
Type rna in any window to start the analysis program.
5.4.3.16.
Autodock
---> LINK TO DOCUMENTATION
Autodock is a flexible docking program, written in the Laboratory of
A. Olson at Scripps.
For detailed information and answers to FAQ, go to the URL
http://www.scripps.edu/pub/olson-web/doc/autodock/.
To perform a docking, type autodock_setup. This will put into your
path the various programs referred to in the manual.
Examples can be found in the directory
/e5share/softlib/prog/modeling/autodock/dist_3.0/examples/ .
5.4.3.17.
Voidoo
---> LINK TO DOCUMENTATION
Voidoo is a program from the
Uppsala Software Factory.
It finds cavities in a molecule and calculates their volume.
To run it, just type voidoo.
5.5.
Sequence analysis programs.
In conjunction with the sequence databases
(see Sec. 4.) we
have programs available that perform the searches, retrievals,
alignments and other specialized tasks. Besides the programs
discussed below, the modeling packages
Quanta,
Insight and
Sybyl
also have extensive sequence analysis capabilities.
5.5.1.
GCG.
--->
LINK TO DOCUMENTATION
GCG is a package of several programs for sequence analysis
running on concave.
To run it, first add the following line to your
.cshrc file (on the SGI's).
use gcg
Then, open an xterm window on one of the graphics workstations
and type:
In addition to the programs in GCG we have the programs
Maligned to display and edit multiple sequence alignments,
and Malform to produce a Postscript hard copy.
To run Maligned, type
@programdisk:[maligned]maligned on msvax.
To run Malform, type
Run programdisk:[maligned]malform_tv.exe on msvax.
5.5.3.
Clustal
---> LINK TO DOCUMENTATION
Clustal is a multiple sequence alignment program.
Tu run it,
type clustal to start
version 1.5b (April, 1997)
5.5.4.
Refine
---> LINK TO DOCUMENTATION
Refine is a program written by Karel Konvicka to
post-process alignments (especially for transmembrane helices) and
make some format conversions. Type refine on the SGI's to
run the program.
5.5.5.
Serratus
Serratus (originally from Oxford Molecular) allows you to
manipulate multiple sequence alignments (e.g., generated by
Clustal) and has a non-redundant sequence database (dated 1992)
that can be queried. Serratus is installed on msvax.
To run Serratus on msvax, execute the commands
oml (can be put in the LOGIN.COM file)
and
delphos for the database query
or
somap for the manipulation of multiple
sequence alignments.
5.5.6.
Matchmaker
Mathcmaker (from Tripos) is installed on the SGI server. It makes
structural predictions from protein sequence based on environmental
homologies as opposed to simple sequence homologies. It is based on
the work of J. Skolnick. There is documentation and a tutorial.
Type matchmaker to run it on an SGI graphics terminal.
5.5.7.
Threader
---> LINK TO DOCUMENTATION
Threader from J. Thorton's group is installed on endo.
It will try to match a query sequence to its own database by a
threading algorithm. To run it with a query sequence in the file
test.seq (most sequence formats are supported), type
threader -j -p test.seq results.out > & log.
5.5.8.
Iditis
Iditis allows you to query an annotated version of the
PDB
based on various structural motifs. It is installed on bonus.
Type iditis to run it through the graphical interface
(only from an X terminal).
To run it in command line mode (from a simple terminal) type
iditis -c .
To run a search in the background type
iditis -c -o -q <query file> -x &
Examples can be found in the directory
OML_IDITIS/EXA (typing iditis will define
OML_IDITIS).
A brief tutorial is also available.
6.
USAGE POLICIES
6.1.
Disk space policies
Since the total disk space is limited on each machine, fair
usage dictates to set limits to the disk space used. These limits
are different for the home directories (that are regularly backed
up by the system) and for the scratch directories:
Note:
the /home and
/scratch filesystems are the ONLY
places where users are allowed to run their jobs. All other
filesystems are restricted for system use. In particular, do not
use /tmp.
/scratch* are shared resources.
They are also a physical entity,
so it is possible (and proven) that one person can fill a /scratch
100% full and this way kill or maim other people jobs.
Current levels of saturation are printed during login - you should
pay attention to those messages.
To prevent
/scratch*'s to fill up, the following policy was agreed
upon:
For special occasions users can use more than the limit.
In those cases:
1) The user must ask the system manager his permission.
2) If there are no other requests made and the need is valid
and there is enough space available, an agreement has to be made
for how much and how long the user can use the given amount of
extra-space.
3) After a given time, the user has to reduce his/hers
disk-usage back to the limit level. If this is not done, disk-quotas
will be established.
6.2.
Job submission policies
At the moment, concave no ques installed. Instead, we are supposed to
limit the number of obs running to 24 (twice the number of CPU's);
To
ensure equitable access to this computational resource
members of the Dept. of Physiology & Biophysics
who have acces to the Farm
are allowed to run one job only;
other users are limited to two jobs per user.
Exceptions can be granted by prior consultation with the system
manager.
Note that the queues (where installed) have time limits
(see Sec. 3.7.).
Jobs on machines without queues run until the next system
shutdown (or crash).
6.3.
Rules for using the Farm.
The computers of the 'avenues' are for the primary use of the Consortion Of
Investigators (COI) who wrote the proposel to fund the Farm.
Major emphasis is placed on creating and running parallel applications.
For the ease of assuring even load on the system,
specific machines are assigned to specific members of the COI:
A list of 'legitimate' users of each machine is maintained in the
file /scratch/priority
Anybody else submitting a job will automatically run with very low priority.
This way idle CPU's can be utilized by anybody, but the 'legitimate'
users can always resume running without having to wait for the
'outsider' job to finish.
The command loadlist lists all jobs running
on the various computers and loadcount lists just
the number of running jobs.
From time to time, users may request more than four CPU's. This should
be arranged in advance with the other COI members.
It is also suggested to limit the number of jobs to four
on each machine to ensure the efficient execution of the parallel jobs.
6.4.
General code of conduct.
As a matter of principle, the Molecular Modeling Core would like
to establish as few rules as possible. Achievement of this goal
requires responsible behavior from everybody's part.
Responsible users
1. familiarize themselves with the capacity of the various
facilities and generally refrain from 'monopolizing' its resources;
2. exit from programs with limited mumber of licenses (e.g., insight, quanta,
matlab) when not using it and
properly log off from the graphics workstations when finished;
3. back up to tapes (see Sec. 3.10.) files
that are not likely
to be used soon (the larger the files the shorter time period is
represented by this 'soon'), compress files that are not needed
immediately and heed periodic backup requests from the system
managers that may appear among the login messages;
4. let the system manager know if they removed any manual or
documentation from Rm 21-87 and generally return them promptly - in
the meantime keep it accessible to others;
5. scrupulously observe the policies related to both the
disk space usage and the job submissions
as spelled out above in sections 6.1.
and 6.2.
Lack of responsible behavior (as defined above) is likely to
result in grumbles of increasing intensity with each occurrence,
mostly from the part of the system manager, but you may hear from
your affected colleagues as well.
Adherence to the disk use policies (as described above in
Sec. 6.1.) is of prime importance since
consuming excessive amount of disk space may lead (and in fact,
several times has lead) to filling up disks and corrupting
jobs running at that time.
Servers and special purpose computers
Hostname Hardware
Location
fulcrum.mssm.edu SGI 2xR10000 Irix 6.5
(21-33)
concave.mssm.edu SGI 12xR10000 Irix 6.5
(21-33)
gprotein.mssm.edu SGI O200 2xR10000 Irix 6.5
(21-33)
msvax.mssm.edu DEC 3000 AXP Model 800S
(13- )
Graphics workstations
Hostname Hardware
Location
prion.mssm.edu SGI R10000 Irix 6.5 GR
21-87
tata.mssm.edu SGI R4400 Irix 6.5 GR
21-60
fermat.mssm.edu SGI R5000 Irix 6.5 GR
21-77B
fermi.mssm.edu SGI R5000 Irix 6.5 GR
21-77B
bonus.mssm.edu SGI R4400 Irix 6.5 GR
21-83
flexi.mssm.edu SGI R5000 Irix 6.5 GR
21-64
cadiz.physbio.mssm.edu SGI Octane Irix 6.5 GR
21-77B
valdez.physbio.mssm.edu SGI Octane Irix 6.5 GR
21-77B
cyclops.physbio.mssm.edu SGI Octane Irix 6.5 GR
21-77B
Parallel systems
Hostname Hardware
Location
york.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
lexington.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
park.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
madison.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
lenox.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
douglass.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
cpw.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
columbus.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
amsterdam.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
westend.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
wall.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
canal.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
prince.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
spring.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
bleeker.physbio.mssm.edu SGI O200 4xR10000 Irix 6.5
(21-33)
eagle1.physbio.mssm.edu Compaq Tru64 UNIX
V5.0A Irix 6.5
(21-33)
eagle2.physbio.mssm.edu Compaq Tru64 UNIX
V5.0A Irix 6.5
(21-33)
eagle3.physbio.mssm.edu Compaq Tru64 UNIX
V5.0A Irix 6.5
(21-33)
eagle4.physbio.mssm.edu Compaq Tru64 UNIX
V5.0A Irix 6.5
(21-33)
eagle5.physbio.mssm.edu Compaq Tru64 UNIX
V5.0A Irix 6.5
(21-33)
batman.physbio.mssm.edu Linux
(21-33)
Hostname vi emacs
edt edit
SGI's yes yes
yes
msvax yes
yes
and <format> can be
Application software is currently found in several different file systems:
Each server for home directories also includes an NIS password file
containg the passwords valid for the systems
whose home directory is in that server.
Home directories are backed up regularly (weekly).
I/O intensive calculations should always use a directory on
(one of) the machine's scratch disk to avoid having to perform the
I/O through the network since their
scratch file system is always
physically on the machine that the calculations are run.
Using the home directory for such calculations would be
likely to be unnecessarily slow and to
unnecessarily increase network traffic.
Eventually, all software will be migrated to /usr/global
Hostname Compile Optimize
Index check Debugger
SGI's f77 -O2 or -O3
-C -g
Alpha's f77 -O4 or -O5
-C -g
Linux f77 or g77 -O4 or -O5
-C -g
Vaxen FOR (optimizes)
/CHECK=BOUNDS
setenv PVM_ROOT /usr/local/c24b1/pvm3_concave/pvm3 (on Concave)
setenv PVM_ROOT /e5share/softlib/prog/util/par/pvm3 (elsewhere)
It is possible to use a drive without being logged on to the
machine that has the tape drive you want (although you need an
account there) - contact the P&BP system manager for the
scripts to do it.
and (sometimes different)
operating systems (see Sec. 2.):
They are only downward compatible (at best),
i.e., newer architectures can run programs
compiled for the older architectures, but not the reverse.
Host GAUSS_EXEDIR
GAUSS_SCRDIR
concave /usr/local/software/g98
/hosts/<hostname>/reserve/<loginid>
farm
/usr/share/gaussian/g98
/hosts/<hostname>/reserve/<loginid>
mepmap <jobname> generates a density contour plot
either as a PostScript file or displayed in an X-window.
The library in Concave /usr/local/software/gamess/graphics contains
additional utilities.
5.5.2.
Maligned, malform
--->
LINK TO DOCUMENTATION
Host Home directory limit
Scratch space limit
SGI's (fulcrum) 400 Mb
Farm (york) 400 Mb
4,000 Mb
concave
4,000 Mb
The CPU's of the 'street' machines are assigned as follows: