Note:
For programs marked with --> DOCU a link is provided
to the documentation kept on line.
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.
1.
Mathematics oriented programs.
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.
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.
1.3.
Numerical Recipes.
The subroutines (source code)
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
in the directories nrecipes/f /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.
2.
General purpose visualization programs.
2.1.
Gnuplot.
DOCUMENTATION
HOME
Platform: SGI/mips
Gnuplot is an interactive plotting package.
It is able to generate
linear, 2D and 3D plots on an X-terminal as well as to create
postscript file.
To execute type gnuplot.
2.2.
XMGR.
DOCUMENTATION
Platform: SGI/mips
XMGR is a general plotting program running on the SGI's, written
in the Witzmann Institute. Newer versions have been renamed to Grace.
Type xmgr to run it.
2.3.
TeX.
Platform: SGI/mips
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.
Type 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 to LaTeX
(in a rudimentary fashion) - see Dr. Mezei if interested in it.
To use TeX/LaTeX on a PC, download
MikTeX
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.
Platform: SGI/mips
The current version is Gaussian-98, revision A7.
The command gaussian jobname
will submit a Gaussian job using the file jobname.g98
as input, and jobname.g98out as output.
Scratch space will be used in the directory called
username (the same as your login id)
on the reserve, scratch or home
file system of the host running the job - it picks the first one available.
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 requires the line %Nproc=N
in the .g98 input file where
N is the number of processors requested.
3.2.
Molcas
DOCUMENTATION
HOME
Platform: SGI/mips
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
/hosts/fulcrum/homes/molmod/src/molcas.
The executables are in the subdirectory bin
and examples can be found in the subdirectory examples.
3.3.
Gamess
DOCUMENTATION
HOME
Platform: SGI/mips
The ab-initio package GAMESS (a descendant of HONDO)
can be run by typing
gamess <JOBNAME> <Number of processors>.
The input data should be in a file called <JOBNAME>.inp .
Like Gaussian, scratch space will be used in the directory called
username on the reserve, scratch or home
filesystems.
There is a directory tests in the gamess distribution directory
(/hosts/fulcrum/homes/molmod/src/gamess)
containing example input files (and described in the
documentation).
3.4.
Gamess graphics utilities
DOCUMENTATION
HOME
Platform: SGI/mips
There are also graphics utilities available in conjunction with Gamess.
For now, they can be found in the directory
/hosts/fulcrum/homes/molmod/src/gamess/graphics.
For example,
mepmap <jobname> generates a density contour plot
either as a PostScript file or displayed in an X-window.
3.5.
Mopac
DOCUMENTATION
Platform: SGI/mips
The command mopac executes Mopac93.
Examples can be found in
/hosts/fulcrum/homes/molmod/src/mopac_93/mopac_examples .
3.6.
Amsol
DOCUMENTATION
Platform: SGI/mips
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,
type amsol < input > output.
Several test input and output files are in the directory
/hosts/fulcrum/homes/molmod/src/amsol
with extensions .dat and.out , respectively.
Platform: SGI/mips
Molekel displays electron density calculated by
GAUSSIAN,
NBO, GAMESS*, Hondo, ADF, prddo.
It can decompose densities to orbital
components.
Type molekel on a graphics terminal.
3.8.
Molden
DOCUMENTATION
HOME
Platform: SGI/mips
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.
Test inputs are in the directory
/hosts/fulcrum/homes/molmod/src/molden3.3/test
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,
VMD,
Rasmol,
Molmol.
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,
BatchMin,
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 logging on to
the requisite host from another computer.
We also have several programs that have been written for a
particular analysis task.
If there is a program you wrote or know of that could be useful,
we can add it to our holdings.
4.1.
Full graphics programs
4.1.1.
InsightII/Discover
HOME
Platform: SGI/mips
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. 4.3.8.).
Platform: SGI/mips
To use Quanta,
type quanta.
Quanta provides an interface to Charmm.
Platform: SGI/mips
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.
Currently, we don't have license for Sybyl.
Platform: SGI/mips
Macromodel is a molecular modeling package originally 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
/hosts/fulcrum/homes/molmod/src/macromodel_v0
- the environmental variable
MMOD_ROOT should point here.
Macromodel can also be run
from a Mac running MacX.
The batch-version (called BatchMin)
can be executed by typing bmin.
The package contains a number of utility programs as well as the program
xcluster that performs cluster analysis on distance
matrices.
4.1.5.
VMD
DOCUMENTATION (HTML)
DOCUMENTATION (PDF)
HOME
Platform: SGI/mips
VMD is a molecular graphics package from the
Theoretical Biophysics Group at
the University of Illinois and Beckman Institute.
Type vmd to run it.
4.1.6.
Grasp
DOCUMENTATION
HOME
Platform: SGI/mips
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.
The program Simulaid
can prepare a charge file from Charmm or Amber topology (RTF) files.
4.1.7. MSV
DOCUMENTATION
Platform: SGI/mips
MSV is a surface visualization program using the molecular surface
computation package
MSMS written by Michael Sanner at Scripps.
It is faster than Grasp.
Type msv to run it.
4.1.8.
Rasmol
Platforms: SGI/mips, Windows, Mac
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
to run it. Help is available at the command line.
It can also be installed on your PC or Mac.
4.1.9.
Molmol
DOCUMENTATION
HOME
Platforms: SGI/mips, Windows
Molmol is a full graphich program from the Wutrich Laboratory
In Zurich.
Besides the documentiation, there is an on-line
tutorial.
4.1.10.
Whatif
Platform: SGI/mips
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.
4.1.11. Molscript
DOCUMENTATION
HOME
Platform: SGI/mips
Molscript, written by Per Kraulis,
creates schematic or detailed molecular graphics images
from molecular coordinates, mostly for protein structures.
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.
4.2.
Batch oriented molecular modeling programs
4.2.1.
Charmm DOCUMENTATION:
V24 text
V26 HTML
DOCU (V27 text)
DOCU (V28 text)
Charmm is the most widely used modeling program at the Core
and several versions of it are available.
Older versions (SGI only):
The toppar directory of the older versions have been placed
into
/hosts/fulcrum/homes/molmod/src/charmm_archive/data/toppar_22
and
/hosts/fulcrum/homes/molmod/src/charmm_archive/data/toppar_23
4.2.2.
Amber
DOCUMENTATION (HTML)
DOCUMENTATION (PDF)
HOME
Platform: SGI/mips
The command use amber
puts into your path the Amber 6.0
executables.
An interactive interface called Leap generates
Amber input files.
On an X-terminal type xleap
(you may have to execute the requisite setenv DISPLAY
command as well) to start it.
Interface front end documentation
Interface documentation
Version 0 is on the SGI server in the directory
/hosts/fulcrum/homes/molmod/src/amber_v0,
4.2.3.
NAMD DOCUMENTATION
HOME
Platform: SGI/mips
NAMD is a fast molecular dynamics program from the
Theoretical Biophysics Group at
the University of Illinois and Beckman Institute.
4.2.4.
CPMD
DOCUMENTATION
Platform: SGI/mips
CPMD is an ab-initio molecular simulation program based
on the Car-Parinello method.
Type cpmd to start the program.
4.2.5.
Modeller
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
Modeller is a program for protein modeling with spatial
restraints written by Andrej Sali. It is most frequently used for
homology or comparative modeling.
Type modeller <command file> to run it.
Test cases are in the directory
/hosts/fulcrum/homes/molmod/src/modeller6v1/scripts
on the SGI server.
The command file should have the extension <top>.
A printed documentation is also available.
4.2.6.
BOSS
DOCUMENTATION
HOME
Platform: SGI/mips
Boss is the Monte Carlo program developed by W.L. Jorgensen.
A sample command file uboptcmd can be found in
/hosts/fulcrum/homes/molmod/src/boss.
4.2.7.
MMC DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
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.
4.2.8.
Delphi
DOCUMENTATION
HOME
Platform: SGI/mips
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.
Type delphi prm > logfile & to run it
where prm is the name of the parameter file.
Example parameter file is in
/hosts/fulcrum/homes/molmod/src/delphi/export99/pti.
4.2.9.
UHBD
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
The command uhbd starts the
University of Houston Brownian Dynamics program dimensioned to use
65x65x65 grid.
Typing uhbd 110 starts (only on the SGI's for now) the version
using a 110x110x110 grid.
Among others, it performs Brownian dynamics simulations and
solves the Poisson-Boltzmann equation.
4.2.10.
Maxwell
DOCUMENTATION
HOME
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.
4.2.11.
Polyrate
DOCUMENTATION
Platforms: SGI/mips, Linux, Alpha/tru64
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 /hosts/fulcrum/homes/molmod/src/polyrate.
4.2.12.
A. Rashin's solvation program
DOCUMENTATION
Platforms: SGI/mips, Linux, Alpha/tru64
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
/hosts/fulcrum/homes/molmod/src/csolvation. The directory
contains sample scripts, as well as the executables and data files.
4.2.13.
Jumna and Ligand
Platform: SGI/mips
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 4.3.2.) or the companion program Nchem.
Ligand can energy minimize a molecule or
a molecular complex.
The commands jumna, ligand and nchemo, respectively, run them.
4.2.14.
Congen
DOCUMENTATION
Platforms: SGI/mips, Linux, Alpha/tru64
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
/hosts/fulcrum/homes/molmod/src/congen
(with test), and the executable is called congen.
4.2.15.
Qpack
DOCUMENTATION
Platform: SGI/mips
The program package Qpack from UCFS (obtained for us by Dr.
Osman) calculates both a 'contact list' and a
residue-based energy for a protein in a given
conformation to quantify the packing efficiency.
5.4.3.
Structure and simulation analysis programs
4.3.1.
hb_ldp
Platform: SGI/mips
Calculates and plots hydrogen-bond distance matrix and linear
distance plot (written by Alan Factor).
Type hb_ldp at any SGI graphics terminal
and answer the questions.
4.3.2.
Curves, Pcurves
DOCUMENTATION
HOME
Platform: SGI/mips
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 (part of
MD Toolchest or
run independently on the SGI server. Type
curves to run it.
4.3.3.
MD Toolchest
DOCUMENTATION
Wesgraph DOCUMENTATION
HOME
Platform: SGI/mips
MD Toolchest is the successor of Dials and Windows from the
Beveridge group at Wesleyan University.
Wesgraph is the associated graphics package.
Examples for both can be found in the Wesleyan
home page
4.3.4.
Plotcorr
DOCUMENTATION
OUTPUT EXAMPLE
Platform: SGI/mips
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>]
4.3.5.
Brookhaven
PDB analysis programs (Procheck)
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
Procheck is a suite of program developed in the laboratory of
Janet M, Thornton.
The command
procheck input.pdb resolution
will run the whole suit and the command
proplot input.pdb resolution runs the program proplot where
input.pdb is the input PDB filename and resolution is the
resolution of the structure (in Å).
4.3.6.
ProsaII (Protein structure analysis)
DOCUMENTATION
HOME
Platform: SGI/mips
ProsaII analyzes a protein structure for potential deficiencies.
Type prosaII (on Cadiz, Valdez or Cyclops only!) to open a window.
Sample session is described in the
manual, starting at page 20.
The test command files are located in
/hosts/fulcrum/homes/molmod/src/ProsaII3.0, and the corresponding PDB files
are in ProsaII's default brookhaven directory,
/hosts/fulcrum/homes/molmod/src/ProsaII3.0/brookhaven .
4.3.7.
Simloc
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
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.
4.3.8.
DSSP
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
DSSP is a widely used program thatassigns secondary structure
elements to protein residues.
It reads in a protein structure in PDB format and
analyzes it for structural motifs.
Type
dssp <input file name> <output filename>
to run it.
4.3.9.
Gepol
DOCUMENTATION
Platforms: SGI/mips, Linux, Alpha/tru64
Gepol is the program of Juan Luis Pascal calculating
molecular surfaces defined in three different ways. The latest
version is in the directory
/hosts/fulcrum/homes/molmod/src/gepol.
The directory also contains older versions and examples.
Type gepol to run it.
4.3.10. MSMS
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.
Type msms to run it.
4.3.11.
Simulaid
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
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.
4.3.12.
Babel
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
Babel is a coordinate file conversion program, able to
interconvert among a number of formats used by popular modeling and
ab initio programs.
Type babel -m to
be presented with the menu and answer the quiz.
4.3.13.
Ligplot, Nucplot, Hbplus
DOCUMENTATION
LIGPLOT
& NUCPLOT HOME
HBPLUS
HOME
Platform: SGI/mips, Linux
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
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.
Additional hydrogen bonds can be defined by the program hbadd
- see the Ligplot documentation for its use.
4.3.14.
Dock
DOCUMENTATION
(ver. 4.0)
ver. 5.1
HOME
Platform: SGI/mips
Dock is a collection of programs that allows the search of a database to find
matches with a target structure.
Version 1 has been installed on the SGI server.
Type dock5 to run it.
Examples are in
/hosts/fulcrum/homes/molmod/src/dock_1.0/demo.
4.3.15.
Rutgers Nucleic Acid Analysis Programs
Platforms: SGI/mips, Linux, Alpha/tru64
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.
The program connolly calculates molecular surfaces.
To run, type
connolly <file1.dat> <file2.dat> <input.dat>
where the three file names contain the three types of data
required by the program.
The directory
/hosts/fulcrum/homes/molmod/src/connolly
contains two files called file1.dat and
file2.dat with default values.
Platforms: SGI/mips.
4.3.17.
Voidoo
DOCUMENTATION
HOME
Platform: SGI/mips
Voidoo is a program from the
Uppsala Software Factory.
It finds cavities in a molecule, calculates their volume and
finds the residues/atoms lining the cavities.
Type voidoo to run it.
4.3.18.
Vega
DOCUMENTATION
HOME
Platform: SGI/mips
Vega was developed to create a bridge between most of the
molecular software packages, like BioDock, Quanta/CHARMm,
InsightII, Mopac, etc. In this tool have been also
implemented some features that are useful to analyze,
display and manage the 3D structures of molecules.
Type vega to run it.
4.3.19
MadBend
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
MadBend (written by Dan Strahs)
is designed to calculate the curvature of DNA,
using as input the base pair roll, tilt and twist values
(calculated, e.g., by Curves).
To run it, type Madbend.
4.3.20.
Mepsi
DOCUMENTATION
Platforms: SGI/mips, Linux, Alpha/tru64
Mepsi, written by Ann Richards, calculates a molecular
similarity index based on the comparison of the respective
electrostatic potential maps.
The two potential descriptor files should be called fort.1 and fort.2, resp.
Typing mepsi executes the program with default input parameters,
typing mepsi <Input file> reads in your own input file.
4.3.21.
Nmrclust
DOCUMENTATION
HOME
Platform: SGI/mips
Nmrclust performs overlaying or clustering a set of molecular structures.
Comparison is based on user-defined atoms.
Type nmrclust to run it.
4.3.22.
Intocham
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux, Alpha/tru64
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
and answer the quizzes.
Contact Dr. Mezei if problems arise - there can be a
number of ambiguities in the type conversions.
4.3.23.
MM_SCP
DOCUMENTATION
A program to calculate Ph dependent electrostatic effects in
biological macromolecules using a microenvironment modulated, screened
Coulomb potential approximation
4.3.24
oc_cluster
DOCUMENTATION
HOME
Platforms: SGI/mips, Linux
Hierarchical clustering program from Geoffrey Barton's Laboratory.
It rquires the upper triangular distance matrix elements as input.
To run it with test.dis as your input file type
SCWRL is a program
for prediction of protein side-chain conformations,
using a new algorithm based on graph theory that
solves the combinatorial problem in side-chain prediction
more rapidly than any other available program.
Type
scwrl3 -i <input_file> -o <output_file>
to run it.
Platforms: SGI/mips.
Linux, Windows, Mac versions available on request
MacroDox,
among others,
Type macrodox to start it.
If you wan to run the Brownian dynamics program bdtirm8.exe
or the PB solver program wwsnl6.exe outside Macrodox
(recommended) then you have to type first
source /hosts/fulcrum/homes/molmod/bin/macrodock_setup.
Tutorial files are in
/hosts/fulcrum/homes/molmod/src/macrodox3/tutor
Platforms: SGI/mips.
4.3.27.
Autodock
DOCUMENTATION
HOME
Platform: SGI/mips
Autodock is a flexible docking program package,
written in the Laboratory of A. Olson at Scripps.
For detailed information and answers to FAQ, go to the URL
http://autodock.scripps.edu
To perform a docking, type
source /hosts/fulcrum/homes/molmod/bin/autodock_setup.
This will put into your
path the various programs referred to in the manual.
Examples can be found in the directory
/hosts/fulcrum/homes/molmod/src/autodock_3.0/examples/ .
Autodock4 is installed on Faradis.
4.3.28.
Fullcreen
DOCUMENTATION
HOME
Fullscreen is a collection of script and small programs to run
virtual screening with Autodock (version 3 or 4).
COntact Dr. Mezei for the latest version.
4.3.29.
Dockres
DOCUMENTATION
HOME
Platform: Unix/Linux
Dockres is a Fortran program to filter sot and analyze the result of
virtual screening with Autodock (version 3 or 4).
COntact Dr. Mezei for the latest version.
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.
5.1.
GCG.
DOCUMENTATION
HOME
GCG is a package of several programs for sequence analysis
running on fulcrum.
Open an xterm window on one of the graphics workstations
and type:
5.2.
Inquiry bioinformatics package
DOCUMENTATION
The Apple BioTeam's Bioinformatics portal is available on Faradis
through a web browser at the URL
http://faradis.mssm.edu.
It requires a login using your regular Faradis user id and password.
a large number of applications are available.
5.3.
Clustal
DOCUMENTATION
HOME
Clustal is a multiple sequence alignment program.
Tu run it,
type clustalw to start
version 1.82 (Feb. 2001)
Platforms: SGI/mips, Linux, Alpha/tru64
5.4.
Refine
DOCUMENTATION
Platforms: SGI/mips, Linux, Alpha/tru64
Refine is a program written by Karel Konvicka to
post-process alignments (especially for transmembrane helices) and
make some format conversions. Type refine to
run the program.
HOME
USE command: use molmod
USE command: use tex-beta
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
Current version (Charmm 27):
Latest version (Charmm28)
USE command: use amber
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use mdtc
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
oc_cluster < test.dis > results.ocout
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod
USE command: use molmod