Scientific Software on the SCS Computers System
The following is an alphabetical list of scientific
software programs installed on the SCS Computers System. The name of the
program is linked to the program homepage. A short description of the
program, taken from the web pages of the vendors, follows. Links to the
start-up instructions page and user manual are provided. For a quick
overview of software, versions and supported platforms see
The Matrix.
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AMBER
is the collective name for a suite of
programs that allow users to carry out molecular dynamics simulations,
particularly on biomolecules. None of the individual programs carries
this name, but the various parts work reasonably well together, and
provide a powerful framework for many common calculations. The term
amber is also sometimes used to refer to the empirical force field that
is implemented here. It should be recognized however, that the code and
force field are separate: several other computer packages have
implemented the amber force field, and other force fields can be
implemented with the amber programs.
- Start-up Instructions
- Online Manual
- PDF manual for Amber
- PDF manual for Amber Interface
- PDF manual for Interface
- PDF manual for Roar
-
ANSIG
is a program for viewing and assigning 2D, 3D and 4D NMR spectra of
biological macromolecules. The input data for the program are frequency-domain
spectrum matrices, together with the sequence of the protein. All processing of
the spectral matrices must have been done before ANSIG can be used to view the
spectra.
- Start-up Instructions
- Online Manual
-
AutoDock
is a suite of programs designed to predict the bound conformation(s) of
flexible ligands to macromolecular targets of known structure, the structure of
protein-protein complexes.
- Start-up Instructions
- Online Manual
- PDF manual
- PS manual
-
Babel
converts between numerous chemical data formats. Input is a data file in one
of approximately 40 formats such as pdb, shellx, xyz. The output is a data file
in another format.
- Start-up Instructions
- Online Manual
-
Cerius2
from Molecular Simulations, Inc is a
software package that provides an easy-to-use simulation and modeling
environment, offering a broad range of scientific application modules for
studying problems in chemistry, materials science, biology and physics. Here is a list of modules maintained by
the SCS computer center.
- Start-up Instructions
- Online Manual (please send
email to if you are
a registered user of InsightII and can not access the documentation)
-
CLUSTAL
is a program for multiple sequence alignment which includes several
modifications to improve results for the alignment of divergent protein
sequences.
- Start-up Instructions
- Online Manual
-
Cn3D
is a viewing and analysis program that provides linked sequence and
three-dimensional displays of macromolecular structures.
- Start-up Instructions
- Online Manual
-
DNMR
includes a series of programs for calculating complex exchange-broadened NMR
spectra.
- Start-up
Instructions
-
DOCK
addresses the problem of docking molecules to each other by exploring ways
in which two molecules, such as a drug and an enzyme or protein receptor, might
fit together.
- Start-up Instructions
For help, please see the
- Online Manual
- PDF Manual
- PS Manual
-
Felix
from Molecular Simulations, Inc is a
program used for data processing, spectral visualization and analysis for all
types of high resolution, one- dimensional to four dimensional, homonuclear and
heteronuclear NMR data.
- Start-up Instructions
- Online Manual
- Online Tutorials
- Command Language Reference
-
GAMESS
is a program for ab initio quantum chemistry that can compute wavefunctions
ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections
available for some of these. Analytic gradients are available for these SCF
functions, for automatic geometry optimization, transition state searches, or
reaction path following. Computation of the energy hessian permits prediction of
vibrational frequencies. A variety of molecular properties, ranging from simple
dipole moments to frequency dependent hyperpolarizabilities may
be computed.
- Start-up Instructions
- GAMESS Manual
- PDF manual
-
Gaussian 03 (& G98)
is used to study molecules and reactions of definite or potential interest,
including both stable species and compounds which are difficult or impossible to
observe experimentally: short-lived intermediates, transition structures, etc.
It can predict energies, molecular structures, vibrational frequencies-along
with the numerous molecular properties that are derived from these three basic
computation types-for systems in the gas phase and in solution, and it can model
them in both their ground state and excited states.
- Start-up Instructions for Gaussian 03
- Start-up Instructions for Gaussian 98
- Online Help
-
(GCG)Genetics Computer Group
is a software package for the analyses of gene and protein
sequences.The GCG package for sequence analysis contains over 100
interrelated software programs. It enables scientists to analyze DNA and
protein sequences by editing, mapping, comparing, and aligning them.
- Start-up Instructions
- Online Manual
-
GRASP (Graphical
Representation and Analysis of Surface Properties)
- is a molecular visualization package which focuses on the mapping of
various properties on the molecular surface.
- Start-up Instructions
- PS Manual (Postscript)
- Online Manual
- Manual (plain text)
-
InsightII
from Molecular Simulations, Inc.
- is a graphical modeling and simulation environment that seamlessly
integrates a wide variety of scientific software for research in the life and
materials sciences.
- Start-up Instructions
- Online Manual (please
send email to if
you are a registered user of InsightII and can not access the online
documentation)
-
MacroModel
- is a molecular modeling software package allows the user to construct and
graphically manipulate both simple and complex chemical structures, to apply
molecular mechanics and dynamics techniques to evaluate the energies and
geometries of molecules in vacuo or in solution, and to display and examine
graphically the results of the modeling calculations.
- Start-up Instructions
- Online Manual
available for v. 7
-
Matlab
- is a high-level programming language designed for numeric computation,
advanced graphics, and visualization.
- Start-up
Instructions
- Online
Help
-
Mathematica
- A comprehensive mathematical computing environment. It can be used as a
sophisticated calculator, an integrated technical programming environment, or to
perform a single task--like analyzing data or solving a tricky differential
equation, or develop an entire solution, prototype, or even an application.
- Start-up
Instructions
- Online Manual
-
MOE
- MOE (Molecular Operating Environment) is a comprehensive software system for Life Science. MOE is a combined Applications Environment and Methodology Development
Platform that integrates visualization, simulation and application development in one package. MOE contains a broad base of scientific applications for general modeling, drug design, homology modeling, library design.
- Start-up
Instructions
-
Molekel
- is an interactive, three-dimensional molecular graphics package, that
represents molecules as wire frame, stick, ball-and-stick, measures atom-atom
distances, angels and torsion angels, can superimpose molecules, calculates and
displays isosurfaces of electron and spin densities as well as molecular
orbitals from the output of various electronic structure calculation programs.
MOLEKEL uses texture mapping to color code any surface according to e.g. the
molecular electrostatic potential, can animate and display vibrational modes,
can animate geometry optimizations, trajectory files and multiple coordinate PDB
files.
- Molekel v.3.04 Start-up Instructions
- Online Manual available for v.3.04
-
Molden
- Displays molecular density from Gaussian and GAMESS. It is capable of
displaying Molecular Orbitals, the electron density and the Molecular minus
Atomic density. Either the spherically averaged atomic density or the oriented
ground state atomic density can be subtracted for a number of standard basis
sets. Molden supports contour plots, 3-d grid plots with hidden lines and a
combination of both.
- Start-up Instructions/dd>
- View/Download Manual(Also available at the computer center.)
-
Molscript
- is a program that will generate very clear, cartoon like, diagrams of
chemical structures. It will do ribbons or ball and stick models for proteins or
smaller chemicals. The output picture is a postscript file. DSSP
calculates a protein's secondary structure and it is usually used in
conjuction with Molscript to produce
protein cartoons. It is also used for creating input files for Raster3D
- Start-up Instructions
- Online Manual
-
NAMD2
- is a parallel, object-oriented molecular dynamics program designed for
high performance molecular dynamics simulations of large biomolecular systems.
- Start-up Instructions
- PDF Manual
- Online User's Manual
- PS Users Guide
- PS Programmers Guide
-
PHYLIP
- is a free package of programs for inferring phylogenies.
- Start-up Instructions
- Online Manual (Web Servers to run PHYLIP over the net)
-
Quanta
- provides a powerful and comprehensive modeling environment for 2D and 3D
modeling, simulation, and analysis of biological macromolecules and small
organics. Functionality includes structural and similarity analysis tools,
cluster analysis, and flexible fitting. Advanced and customizable graphics
display assists understanding of even the most complex molecular systems.
Simulation and analysis results are presented as clear plots and graphs. With
access to all standard file formats, and interfaces to CHARMm, MODELER, and
multiple third party QM/MM codes, QUANTA offers a complete solution for
visualization and investigation of molecules in the life sciences.
- Start-up Instructions
- Quanta Online Manual
- CHARMm Online Manual
- (please send email to if you are a
registered user of Quanta/CHARMm and can not access the online documentation)
-
Raster3D
- is a set of tools for generating high quality raster images of
proteins or other molecules. The core program renders spheres,
triangles, cylinders, and quadric surfaces with specular
highlighting, Phong shading, and shadowing. Raster3D can also be used
to render pictures composed in other programs such as Molscript in
glorious 3D with highlights, shadowing, etc.
- Start-up
Instructions
- Online
Manual
- Manual
in PDF format
-
RasMol
- A very simple program used for molecular visualization.
- Start-up Instructions
- Online Manual for Rasmol v2.6
- Online Manual for Rasmol v2.7.1
-
Spartan
- This program is a molecular modeling package that specializes in
electronic structure calculations, including ab initio, density functional
theory, semi-empirical, molecular mechanics, similarity analysis, conformational
analysis, and property calculations including
QSAR. The package has a graphical interface that can also be used to set-up Gaussian94 calculations.
the SCS has two versions of spartan. The 'old' Spartan 5.1 for Unix, and the 2002 new
version of Spartan, Spartan02 Full Version, for Unix and PCs in he vizlab.
Spartan02 for Windows can be installed on your PC. Contact ( ) to see if hardware keys are available.
- Start-up
Instructions
- Online
description of available computational methods (CANS has the FULL version, i.e., methods in red on the web page are available to us.
-
Tutorial and User's guides books are available for check-out at the Computer Center contact
-
SHELX (X-Ray Refinement)
- is a set of programs for crystal structure determination from single-crystal diffraction data.
- Start-up instructions
- Manual in PDF format
- Shelx FAQ
-
VMD (Visual Molecular
Dynamics)
- is a molecular visualization program for displaying and animating large
biomolecular systems using 3-D graphics.
- Start-up Instructions
- PDF Manual
- Online Manual
-
X-Plor 3.1
- is a large computational system for X-Ray Crystallography and NMR. It
stands for exploration of conformational space of macromolecules restrained to
regions allowed by combinations of empirical energy functions and experimental
data. But it also stands for exploration of modern concepts of structured
programming in macromolecular simulation.
- X-PLOR startup
instructions
- Online
Manual from Yale
- Online Manual from MSI
(please send email to if you are a registered user of Quanta/CHARMm and can not access the online documentation)
