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Category: Molecular Modeling

Programs for the creation, manipulation and viewing of molecular models.

Amber

Description

AMBER:Assisted Model Building with Energy Refinement

AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

Home Page

http://amber.scripps.edu

Tutorial

Amber Tutorials

Documentation

Remote online documentation can be found on the Amber 7 Manuals and Amber 8 Manuals

Setting Up Your Environment

There are several versions of Amber: serial version, shared-memory parallel (multiprocessor) version (MP) and parallel version that uses MPI message-passing library. The MP version is only available on multi-processor SGI computers. The MPI version is available on SGI Origin computers.
Note: Although serial and parallel versions share most of the code base, there are significant differences. In some cases, parallel version may not produce the same results as the serial version. The results for any new problem obtained with a parallel version should be carefully checked against the serial version. The two parallel verions, MP and MPI, are also significantly different from each other. The MP versions supports a richer set of features, but MPI version may provide better performance in certain cases. The MP version is generally more reliable. You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated files. To do this, enter the following commands:
To initialize serial version 8 of Amber: module add amber/amber8
To initialize serial version 7 of Amber: module add amber/amber7
Only Sander and Gibbs are parallelized in amber.
To access serial sander and gibbs, use command "sander_ser" and "gibbs_ser".
To acess parallel sander and gibbs, use the command "sander_par" and "gibbs_par".
If you access this package on a regular basis, you can add the above lines to your ~/.cshrc file so that your environment will be initialized for Amber every time you log in.

Version: v7.0, v8.0
Labs: IBM SP, IBM regatta, Scientific Development and Visualization Lab, Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all UNIX workstations and servers
Categories: Molecular Modeling, Chemistry, NMR, Molecular Simulation

AutoDock

Description

From the AutoDock documentation:

"AutoDock is a suite of programs designed to predict the bound conformation(s) of a flexible ligand to a macromolecular target of known structure, like an enzyme or DNA. AutoDock has also been used in the prediction of the structure of protein-protein complexes. AutoDock has found application in the computer-aided design of bioactive compounds and in the prediction of peptide binding to antibodies."

Home Page

http://www.scripps.edu/pub/olson-web/doc/autodock/

Tutorial

Some Examples and test systems can be found at the : AutoDock Home Page

Documentation

Remote online documentation can be found on the AutoDock Home Page.
Local documentation including a postscript and html formatted manuals can be found in /usr/local/autodock/doc/

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated files. To do this, enter the following command:
module add autodock
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for AutoDock every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add autodock 
  endif
  ...

Running AutoDock

Once you have setup your environment, the following commands are available:
autodock3
autogrid3
addsol

Version: v3.0.3
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling

AutoDockTools

Description

AutoDockTools, ADT - Tools to Set Up, Run and Analyze AutoDock Dockings.
AutoDockTools, or ADT, is the ultimate GUI to set up, launch and analyze AutoDockruns. With ADT, you can:
- View molecules in 3D, rotate & scale in real time.
- Add all hydrogens or just non-polar hydrogens.
- Assign partial atomic charges to the ligand and the macromolecule (Gasteiger or Kollman United Atom charges).
- Merge non-polar hydrogens and their charges with their parent carbon atom.
- Set up rotatable bonds in the ligand using a graphical version of AutoTors.
- Set up the AutoGrid Parameter File (GPF) using a visual representation of the grid box, and slider-based widgets.
- Set up the AutoDock Parameter File (DPF) using forms.
- Launch AutoGrid and AutoDock.
- Read in the results of an AutoDock job and graphically display them.
- View isocontoured AutoGrid affinity maps.

Home Page

http://www.scripps.edu/pub/olson-web/doc/autodock/tools.html#ADT

Tutorial

AutoDock with AutoDockTools Tutorial can be found here

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated files. To do this, enter the following command:
source /usr/local/autodocktools/cshrc

Running AutoDock

Once you have setup your environment, the following commands are available:
adt
pmv

Version: version 1.1
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling

BABEL

Description

Babel is a program designed to interconvert a number of file formats currently used in molecular modeling.

Babel will read the following file types :

Alchemy                  AMBER PREP               Ball and Stick           
Biosym .CAR              Boogie                   Cacao Cartesian          
Cambridge CADPAC         CHARMm                   Chem3D Cartesian 1       
Chem3D Cartesian 2       CSD CSSR                 CSD FDAT                 
CSD GSTAT                Feature                  Free Form Fractional     
GAMESS Output            Gaussian Z-Matrix        Gaussian Output          
Hyperchem HIN            MDL Isis                 Mac Molecule             
Macromodel               Micro World              MM2 Input                
MM2 Ouput                MM3                      MMADS                    
MDL MOLfile              MOLIN                    Mopac Cartesian          
Mopac Internal           Mopac Output             PC Model                 
PDB                      Quanta                   ShelX                    
Spartan                  Spartan Semi-Empirical   Spartan Mol. Mechanics   
Sybyl Mol                Sybyl Mol2               Conjure                  
Maccs 2d                 Maccs 3d                 UniChem XYZ              
XYZ                      XED

Babel will write the following file types :

Alchemy                  Ball and Stick           Batchmin Command         
Cacao Cartesian          Cacao Internal           CAChe MolStruct          
Chem3D Cartesian 1       Chem3D Cartesian 2       ChemDraw Conn. Table     
Conjure                  Conjure Template         CSD CSSR                 
Feature                  Fenske-Hall ZMatrix      Gamess Input             
Gaussian Cartesian       Gaussian Z-matrix        Gaussian Z-matrix tmplt  
Hyperchem HIN            Icon 8                   IDATM                    
Mac Molecule             Macromodel               Micro World              
MM2 Input                MM2 Ouput                MM3                      
MMADS                    MDL Molfile              Mopac Cartesian          
Mopac Internal           PC Model                 PDB                      
Report                   Spartan                  Sybyl Mol                
Sybyl Mol2               MDL Maccs file           XED                      
UniChem XYZ              XYZ

Home Page

http://smog.com/chem/babel

README

http://smog.com/chem/babel/README

Documentation

Information on how to use babel can be found in http://www.msi.umn.edu/software/babel/manual/docs.txt

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated fils. To do this, enter the following command:
module add babel
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for BABEL every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add babel 
  endif
  ...

Running BABEL

Once you have setup your environment, use the following command to run BABEL with a menu interface
babel -m
Look at the documentation for other options.

Version: v1.6
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations. all sun workstations at VWL
Categories:Chemistry, Molecular Modeling, NMR, X-ray Crystallography

CAChe

Description

CAChe is a computer-aided chemistry modeling package for experimental chemists conducting research in life sciences, materials and chemicals, as well as for undergraduate and graduate educators. The software utilizes semiempirical method for evaluation of heat of formation and geometry optimization as well as for modeling of molecules with up to 20,000 atoms.
For more information, please visit http://www.cachesoftware.com.

Version: v6.1.1 (2003 distribution)
Labs: Basic Sciences Computing Lab, Scientific Development and Visualization Lab, Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all PC's and Mac's at BSCL, SDVL and VWL
Categories: Molecular Modeling, Chemistry

CCP4

Description

The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. They have been collected and developed under the auspices of the Collaborative Computing Project Number 4, in Protein Crystallography, supported by the UK Science and Engineering Research Council (serc) since 1979 and currently the Biotechnology and Biological Sciences Research Council (bbsrc), and coordinated at Daresbury Laboratory. The Project aimed to support collaboration between those working on such software in the UK, and to assemble a comprehensive collection of it to satisfy the computational requirements of the relevant UK groups. The results of this effort are also made available for distribution to academic and commercial users outside the UK. The distribution, described herein, is often loosely referred to as `CCP4', but is properly `The CCP4 Suite'.

Home Page

http://www.ccp4.ac.uk/main.html

Documentation

Online documentation is available at http://www.ccp4.ac.uk/docs.html.

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated fils. To do this, enter the following command:
source /usr/local/ccp4/ccp4-4.2/ccp4.setup
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for CCP4 every time you log in.
eg:
  ...
  # source ccp4.setup when avaialable

  if( -e /usr/local/ccp4/ccp4-4.2/ccp4.setup ) then
     source /usr/local/ccp4/ccp4-4.2/ccp4.setup
  endif
  ...

Running CCP4

Once you have setup your environment, use the following command to run the graphical interface of CCP4:
ccp4i

Version: v4.2
Labs:Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Chemistry, Molecular Modeling

CNS

Description

From the CNS web page:
Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.

Home Page

http://cns.csb.yale.edu

Tutorial

None yet available.

Documentation

After you initialize your environment (see below), an online manual is available by using the cns_web command.

Setting Up Your Environment

You must enter the following command to initialize your environment for CNS:
source /usr/local/cns/cns_solve_1.1/cns_solve_env
If you run this package often, you can add this line to your ~/.cshrc so that it is automatically started whenever you login.

Running CNS

After you have initialized your environment, to run CNS as an interactive session
cns_solve
To run an non-interactive session (majority of usage)
cns_solve < inputfile > outputfile

Version: v1.1
Labs: Basic Sciences Computing Lab
System(s): all SGI workstations
Categories:Chemistry, NMR, X-ray Crystallography, Molecular Modeling

Cambridge Structural Database

Summary

The Cambridge Structural Database (CSD) is the the largest searchable database of experimentally determined crystal structures and is maintained by the the Cambridge Crystallographic Data Center (CCDC). The complete CSD system includes the database as well as the following graphical search, retrieval and data visualisation software:

Program Description Executable

ConQuest 1, 2 and 3D searching of the CSD with very nice interface cq

QUEST 1, 2 and 3D searching of the CSD questv5

VISTA Statistical analysis and graphical display vista

PreQuest Creating Quest searchable databases, in-house prequest

Program	Description	Executable
ConQuest	1, 2 and 3D searching of the CSD with very nice interface	`cq`
QUEST	1, 2 and 3D searching of the CSD	`questv5`
VISTA	Statistical analysis and graphical display	`vista`
PreQuest	Creating Quest searchable databases, in-house	`prequest`

Documentation

online at http://www.ccdc.cam.ac.uk/support/csd_doc/zdocmain.html

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the CSD package uses to access the programs and database. To do this, enter the following command:
module load cambridge
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for the CSD every time you log in.

Version: v5.25 (November 2003 distribution)
Labs: Basic Sciences Computing Lab, Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI and Sun workstations and PC at VWL, BSCL, SDVL
Categories: Molecular Modeling, X-ray Crystallography

Cerius2

Cerius2 provides an easy-to-use molecular modeling and simulation environment, offering a broad range of scientific applicaiton modules.

The following modules are available to MSI researchers:

Package Concurrent Users Description (from the Accelrys, Inc. web site)
Visualizer 3 Cerius2 Visualizer provides a comprehensive modeling environment for building, editing and visualizing models of molecular structure as well as the core requirements for running Cerius2 applications.

Compass 1
Compass is the new version of the PCFF forcefield - the first forcefield parameterized and validated using condensed phase properties. Enables accurate simulation of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases.

Amorphous builder 1
Amorphous builder is used to build models of amorphous polymers and polymer/solvent systems. Combined with simulation and analysis functionality, this offers a powerful way to understand the relationship between amorphous structure and properties.

Compass 1 Compass is the new version of the PCFF forcefield - the first forcefield parameterized and validated using condensed phase properties. Enables accurate simulation of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases.

Conformers 2 Provides conformational search algorithms and associated analysis tools, allowing you to characterize molecular conformation and flexibility, and gain insight into geometric and energetic properties.

Crystal Builder 2 Crystal Builder is used to build and visualize models of inorganic or molecular crystals, helping you to understand crystalline structure and simulate the behavior of solids.

Diffraction 2
Diffraction-Crystal simulates powder, fiber, and single crystal diffraction from crystalline models, which helps you interpret experimental data from molecular, inorganic, and polymeric crystalline materials.

Discover 10
Discover is a user interface to the widely used and well-validated Discover simulation code. Discover provides a broad range of simulation methods, enabling structural characterization and property prediction for molecules, materials, and biological compounds.

Dynamics 2
Dynamics applies molecular mechanics to study structure relaxation and investigate the behavior of a material over a time period. Properties which can be deduced include: stability, diffusion, radial distribution functions and structure factors, and velocity auto-correlation functions.

Force Field Editor 2
Force Field Editor lets you adapt force fields from the Cerius2 database or create your own. You can apply force fields from the literature to your problems and develop and validate in-house parameterizations.

Gaussian 1
Gaussian interfaces to the Gaussian code allowing you to apply ab initio, semi- empirical, and density functional techniques to study the energetics, structure, and chemistry of molecules and transition states.

Mechanical Properties 1
Mechanical Properties predicts a range of ideal elastic modulii for any materials type, helping you to design novel crystalline and amorphous polymers, ceramics, and semiconductors.

Minimizer 2
Minimizer predicts low-energy structures using molecular mechanics calculations and the power of Cerius2's Open Force Field. C2.Minimizer helps you to gain increased understanding of molecular, macromolecular, amorphous, crystalline, and surface structure and properties.

Mopac 1
Mopac interfaces to the popular semi-empirical quantum code MOPAC. You can study molecular structure and energetics, and compute properties such as molecular orbitals and charges.

Morphology 2
Morphology predicts and analyzes the morphology of crystals from their internal crystal structure, which helps you relate morphological features to structure and understand the likely effects of solvents and growth modifying additives.

OFF 2
OFF (Open Force Field) provides molecular mechanics force fields to support Cerius2's property prediction modules. You can choose from an extensive database of force fields covering organics, polymers, zeolites, organometallics, and other materials types.

Powder Indexing 2 Powder Indexing completes a comprehensive package of software modules for crystal structure determination from powder data. You can establish unit cell and symmetry information and use this to assist Rietveld refinement or crystal structure predictions.

Sorption 1 Sorption predicts the adsorption properties of molecules in microporous solids, such as zeolites, helping you to predict adsorption isotherms, binding sites, adhesion energies, diffusion paths, and molecular selectivity.

Surface Builder 2 Surface Builder is used to build 2D periodic models that enable you to investigate surface chemistry, structure, and interactions.

Package	Concurrent Users	Description (from the Accelrys, Inc. web site)
Visualizer	3	Cerius2 Visualizer provides a comprehensive modeling environment for building, editing and visualizing models of molecular structure as well as the core requirements for running Cerius2 applications.
Compass	1	Compass is the new version of the PCFF forcefield - the first forcefield parameterized and validated using condensed phase properties. Enables accurate simulation of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases.
Amorphous builder	1	Amorphous builder is used to build models of amorphous polymers and polymer/solvent systems. Combined with simulation and analysis functionality, this offers a powerful way to understand the relationship between amorphous structure and properties.
Compass	1	Compass is the new version of the PCFF forcefield - the first forcefield parameterized and validated using condensed phase properties. Enables accurate simulation of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases.
Conformers	2	Provides conformational search algorithms and associated analysis tools, allowing you to characterize molecular conformation and flexibility, and gain insight into geometric and energetic properties.
Crystal Builder	2	Crystal Builder is used to build and visualize models of inorganic or molecular crystals, helping you to understand crystalline structure and simulate the behavior of solids.
Diffraction	2	Diffraction-Crystal simulates powder, fiber, and single crystal diffraction from crystalline models, which helps you interpret experimental data from molecular, inorganic, and polymeric crystalline materials.
Discover	10	Discover is a user interface to the widely used and well-validated Discover simulation code. Discover provides a broad range of simulation methods, enabling structural characterization and property prediction for molecules, materials, and biological compounds.
Dynamics	2	Dynamics applies molecular mechanics to study structure relaxation and investigate the behavior of a material over a time period. Properties which can be deduced include: stability, diffusion, radial distribution functions and structure factors, and velocity auto-correlation functions.
Force Field Editor	2	Force Field Editor lets you adapt force fields from the Cerius2 database or create your own. You can apply force fields from the literature to your problems and develop and validate in-house parameterizations.
Gaussian	1	Gaussian interfaces to the Gaussian code allowing you to apply ab initio, semi- empirical, and density functional techniques to study the energetics, structure, and chemistry of molecules and transition states.
Mechanical Properties	1	Mechanical Properties predicts a range of ideal elastic modulii for any materials type, helping you to design novel crystalline and amorphous polymers, ceramics, and semiconductors.
Minimizer	2	Minimizer predicts low-energy structures using molecular mechanics calculations and the power of Cerius2's Open Force Field. C2.Minimizer helps you to gain increased understanding of molecular, macromolecular, amorphous, crystalline, and surface structure and properties.
Mopac	1	Mopac interfaces to the popular semi-empirical quantum code MOPAC. You can study molecular structure and energetics, and compute properties such as molecular orbitals and charges.
Morphology	2	Morphology predicts and analyzes the morphology of crystals from their internal crystal structure, which helps you relate morphological features to structure and understand the likely effects of solvents and growth modifying additives.
OFF	2	OFF (Open Force Field) provides molecular mechanics force fields to support Cerius2's property prediction modules. You can choose from an extensive database of force fields covering organics, polymers, zeolites, organometallics, and other materials types.
Powder Indexing	2	Powder Indexing completes a comprehensive package of software modules for crystal structure determination from powder data. You can establish unit cell and symmetry information and use this to assist Rietveld refinement or crystal structure predictions.
Sorption	1	Sorption predicts the adsorption properties of molecules in microporous solids, such as zeolites, helping you to predict adsorption isotherms, binding sites, adhesion energies, diffusion paths, and molecular selectivity.
Surface Builder	2	Surface Builder is used to build 2D periodic models that enable you to investigate surface chemistry, structure, and interactions.

To run cerius2, you must first set some environment varibles. This is easy. Just type

source /usr/local/cerius/cshrc

Now type

cerius2

For more information, see http://www.accelrys.com/cerius2.
For online documentation, see http://www.accelrys.com/doc.

Version: 4.9
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Chemistry, Molecular Modeling, X-ray Crystallography, Molecular Simulation

Chime

From the Chime home page:

To facilitate the exchange of chemical information globally, MDL provides the Chemscape Chime Web browser plug-in free of charge. Chemscape Chime allows scientists to view chemical graphics directly on an HTML page.
Chime supports most of the popular structure display formats that scientists use including MDL Information Systems' Molfile and Rxnfile and many of the popular 3D display formats such as the Brookhaven Protein Databank (PDB) format (3D rendering and RasMol scripting code courtesy of Roger Sayle.)

NOTE: This plug-in is for 8-bit color graphics displays. For 24-bit systems you must use the Netscape command line option "-visual pseudocolor". Most SDVL and BSCL workstations have 24-bit graphics.

Version: 0.9e
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): all SGI workstations
License: Freeware
Categories: Visualization, Molecular Modeling

Dock

DOCK addresses the problem of "docking" molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together. Compounds which dock to each other well, like pieces of a three-dimensional jigsaw puzzle, have the potential to bind. So, why is it important to able to identify small molecules which may bind to a target macromolecule? A compound which binds to a biological macromolecule may inhibit its function, and thus act as a drug.

DOCK generates many possible orientations (and more recently, conformations) of a putative ligand within a user-selected region of a receptor structure. These orientations may be scored using several schemes designed to measure steric and/or chemical complementarity of the receptor-ligand complex. These scores may be used to evaluate likely orientations of a single ligand, or to rank molecules from a database.

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the CSD package uses to access the programs and database. To do this, enter the following command:
module load dock

Running dock

Once you have setup your environment, use the following command to run dock
dock

Version: 4.0
Labs: Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling

For on-line documentation, please visit http://www.cmpharm.ucsf.edu/kuntz/dock.html.

FTDOCK

Description

FTDOCK is a software package consisting of the main docking program plus one preprocessor and one postprocessor. The primary program, called FTDOCK, accepts two PDB format structure files as input and performs rigid-body docking. The Fourier correlation algorithm used by FTDOCK takes advantage of the fast Fourier transform (FFT) to scan rapidly the translational binding space of two rigid molecules.

Home Page

http://bonsai.lif.icnet.uk/ftdock/ftdock.html

Tutorial

A tutorial is available in the manual.

Documentation

A postscript formatted manual is available here or from the FTDOCK home page.

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated fils. To do this, enter the following command:
module add ftdock
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for FTDOCK every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add ftdock 
  endif
  ...
To use this software on an SGI Origin, you must increase the stack size from the default. For example:
limit stacksize 524288

Running FTDOCK

Once you have setup your environment, use the following command to run FTDOCK
predock
ftdock

Version: v1.0
Labs:Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Chemistry, Molecular Modeling

GRASP

Description

GRASP is a molecular visualization and analysis program by Anthony Nicholls of Columbia University. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties.

Home Page

http://tincan.bioc.columbia.edu/grasp/

Tutorial

Example scripts and macros can be found in:
  /usr/local/grasp/example_scripts_and_macros/
  

Documentation

Versions of the manual in ASCII, Microsoft Word, and PostScript can be found in:
  /usr/local/grasp/manuals/
  
An HTML version of the manual can be found at the GRASP Home Page

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and database. To do this, enter the following command:
module add grasp
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for the CSD every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add grasp 
  endif
  ...

Running GRASP

Once you have setup your environment, use the following command to run GRASP
grasp

Version: v1.2
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling

Gaussian03

Description

Gaussian 03 performs semiempirical and ab initio molecular orbital (MO), density functional, and molecular mechanics calculations.

Documentation

www.gaussian.com

Running

www.msi.umn.edu/software/gaussian03/details.html

First load the Guassian03 module
Next run the qg03 submission script
for submitting the Gaussian job, input_file, to the queue. The command
prints out the options list for the qg03 command.

Version:03 Revision B.01
Labs: IBM Power4, IBM SP, Basic Sciences Computing Lab
System(s): All UNIX workstations and servers
Categories: Chemistry, Molecular Modeling, NMR

Gaussian94

Description

Gaussian 94 performs semiempirical and ab initio molecular orbital (MO), density functional, and molecular mechanics calculations.

Versions

Running

www.msi.umn.edu/software/gaussian94/details.html

First load the Guassian94 module

module load g94

Next launch the executable

rg94 input_file

qg94 [options] input_file

qg94 -h

qg94

Version:94 release D.2
Labs: IBM SP
System(s): IBM SP
Categories: Chemistry

HBPLUS

Description

HBPLUS is a hydrogen bond calculation program from University College Londen. It features include but are not limited to:

Calculates the Geometries of all Hydrogen Bonds
Optionally Lists of Neighbour Interactions
Calculates Hydrogen Positions
Deals with Hydrogens that can Occupy More Than one Position
Optionaly includes amino-aromatic H-bonds.
Supports Full Customisation, eg of

H-bond criteria
Donor and Acceptor Atom Types

Analyses H-bonding Near Asn, Gln and His Side-Chains and
Suggests Optimal Conformations
Supports .hbplusrc Files
Outputs PDB File Including Extrapolated Polar Hydrogen Positions

Home Page

http://www.biochem.ucl.ac.uk/~mcdonald/hbplus/home.html

Tutorial

None at this time.

Documentation

An ASCII (Text) formated manual can be found in:
  /usr/local/hbplus/manual/hbplus.man
  

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and database. To do this, enter the following command:
module add hbplus
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for the CSD every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add hbplus 
  endif
  ...

Running HBPLUS

Once you have setup your environment, use the following command to run HBPLUS
hbplus

Version: v3.15
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling

LIGPLOT

Description

LIGPLOT automatically generates schematic diagrams of protein-ligand interactions for a given PDB file. The interactions shown are those mediated by hydrogen bonds and by hydrophobic contacts.

Home Page

http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html

Tutorial

None at this time

Documentation

An Online Manual is available.

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and database. To do this, enter the following command:
module add ligplot
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for the CSD every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add ligplot 
  endif
  ...

Running LIGPLOT

Once you have setup your environment, use the following command to run LIGPLOT
ligplot

Version: v4.0
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling

MODELLER

Description

From the MODELLER manual:
"MODELLER is a computer program that models protein 3D structure by satisfaction of spatial restraints.
MODELLER is most frequently used for homology or comparative protein structure modeling: The user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate an all-atom model."

Home Page

http://guitar.rockefeller.edu/modeller/modeller.html

Tutorial

Found on MODELLER Documentation Page

Documentation

HTML and Postscript formatted manuals can be found on MODELLER Home Page

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated fils. To do this, enter the following command:
module add modeller
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for MODELLER every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add modeller 
  endif
  ...

Running MODELLER

Once you have setup your environment, use any of the MODELLER programs. eg
mod modscipt
will run MODELLER using the commands in the script file named "modscript"

Version: v4
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling

MOE

Description

The Molecular Operating Environment is the next generation of chemical computing software. MOE is an integrated Applications Environment and Methodology Development Platform. MOE integrates visualization, simulation and application development in one package.

Documentation

Additional details and documentation regarding MOE can be found at www.chemcomp.com.

Running

First load the MOE module

module load moe

Next launch the executable

moe

Version:2005.08
Labs:Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): all SGI and SUN workstations
Categories: Bioinformatics, Chemistry, Molecular Modeling

MacroModel

MacroModel consists of several programs. Macromodel is one of the programs and is used to build, manipulate and display organic chemical structures. BatchMin is a non-interactive, batch-mode modeling program used to minimize the energy of one structure or a series of structures, to eliminate duplicate conformations and to conduct molecular dynamics simulations with calculation of average enthalpy. BatchMin is called by MacroModel and is its use is usually transparent. However, for advanced applications, an understanding of BatchMin may be necessary. MacroModel can read files in its own format and PDB files. Manuals for MacroModel and BatchMin are in the Technical Documentation Center. Online help from within MacroModel is also available. Further information about Macromodel may be obtained from the MacroModel Home Page

MacroModel now uses Maestro as a common graphical user interface. To find out more, please refer to Maestro software documentation.

Version: 8.1
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Chemistry, Molecular Modeling, X-ray Crystallography, Molecular Simulation

Maestro

The Maestro is graphical user interface (GUI) for a series of products from Schrodinger. For brief description of current licensed schrodinger software, please see below for further information

The following modules are available to MSI researchers:

Package Concurrent Users Description (from the Schrodinger, Inc. web site)
Maestro unlimited The Maestro is graphical user interface (GUI) for a series of products from Schrodinger such as impact, jaguar, mac romodel and minta. It allows users to interact both graphically and textually and allows the user to create and di splay complex chemical structures, start and monitor a variety of calculations, and analyze structures and results of calculations.

Qsite 22
QSite is a new mixed mode QM/MM program for highly accurate energy calculations of protein-ligand intera ctions in the active site. The program is specifically designed for proteins and allows a number of diff erent QM/MM boundaries for residues in the active site. QSite uses the power and speed of Jaguar to perf orm the quantum mechanical part of the calculations and OPLS-AA to perform the molecular mechanical part of the calculations.

Jaguar 22
Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory. Jaguar's speed and power make it possible to study larger systems than ever before, or to study many more systems than previously possible, within a reasonable timeframe.

Macromodel 44
MacroModel is a general-purpose package for performing molecular mechanics for small and medium-sized organic molecules in both gas and solution phases. MacroModel has powerful utilities for exploring proteins and protein-ligand complexes. The program offers state-of-the art techniques for evaluating energy, sampling conformations, and accounting for solvation.

Minta 32
Minta allows for efficient calculation of free energy of molecular complexes as well as for individual ligands. Based on conformational analysis, Minta provides direct evaluation of free energies without recourse to long simulations or computational alchemy.

Package	Concurrent Users	Description (from the Schrodinger, Inc. web site)
Maestro	unlimited	The Maestro is graphical user interface (GUI) for a series of products from Schrodinger such as impact, jaguar, mac romodel and minta. It allows users to interact both graphically and textually and allows the user to create and di splay complex chemical structures, start and monitor a variety of calculations, and analyze structures and results of calculations.
Qsite	22	QSite is a new mixed mode QM/MM program for highly accurate energy calculations of protein-ligand intera ctions in the active site. The program is specifically designed for proteins and allows a number of diff erent QM/MM boundaries for residues in the active site. QSite uses the power and speed of Jaguar to perf orm the quantum mechanical part of the calculations and OPLS-AA to perform the molecular mechanical part of the calculations.
Jaguar	22	Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory. Jaguar's speed and power make it possible to study larger systems than ever before, or to study many more systems than previously possible, within a reasonable timeframe.
Macromodel	44	MacroModel is a general-purpose package for performing molecular mechanics for small and medium-sized organic molecules in both gas and solution phases. MacroModel has powerful utilities for exploring proteins and protein-ligand complexes. The program offers state-of-the art techniques for evaluating energy, sampling conformations, and accounting for solvation.
Minta	32	Minta allows for efficient calculation of free energy of molecular complexes as well as for individual ligands. Based on conformational analysis, Minta provides direct evaluation of free energies without recourse to long simulations or computational alchemy.

For more information, please visit
http://www.schrodinger.com.

To initialize serial 2004 release of Maestro:

module add schrodinger/2004

To initialize serial 2005 release of Maestro:

module add schrodinger/2005

Labs:Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI and linux workstations
Categories:Chemistry, Molecular Modeling, X-ray Crystallography, Molecular Simulation

Material Studio

MS Modeling is Materials Studio's modeling and simulation product suite, and is designed for structural and computational researchers in chemicals and materials R&D who need to perform expert-level modeling and simulations tasks in an easy to learn yet powerful environment. It provides flexible and validated tools for the study of materials at various length and time scales.

The following modules are available to MSI researchers:

Package Concurrent Users Description (from the Accelrys, Inc. web site)
MS Visualizer 2 MS Visulaizer - the core MS Modeling product, provides all of the tools that are required to construct graphical models of molecules, crystalline materials, and polymers. Additionally, the Visualizer lets you view and analyze these models and provides the software infrastructure and analysis tools to support the full range of Materials Studio products.

Amorphous Cell 1
Model construction and property prediction for amorphous materials particularly polymers.

Compass 1
A powerful molecular mechanics force field supporting simulations of solid materials.

Discover 1
molecular mechanics and dynamics methods for structure and property prediction.

Dmol 1
DMol3 - a unique density functional theory quantum mechanical code for gas phase, solvent, and solid state simulations.

Forcite 1
An advanced classical molecular mechanics tool, which allows fast energy calculations and reliable geometry optimization of molecules and periodic systems.

Polymorph Predictor 1 Polymorph Predictor - for the prediction of potential polymorphs of a given compound directly from the molecular structure.

Reflex 1 Reflex - powder diffraction simulation enhanced with indexing and refinement capabilities.

X-Cell 1 X-Cell - a novel and robust indexing program for medium- to high-quality powder diffraction data obtained from X-ray, neutron, and electron radiation sources.

For more information, see
http://www.accelrys.com/mstudio/ms_modeling.

For online documentation, see
http://www.accelrys.com/doc.

Package	Concurrent Users	Description (from the Accelrys, Inc. web site)
MS Visualizer	2	MS Visulaizer - the core MS Modeling product, provides all of the tools that are required to construct graphical models of molecules, crystalline materials, and polymers. Additionally, the Visualizer lets you view and analyze these models and provides the software infrastructure and analysis tools to support the full range of Materials Studio products.
Amorphous Cell	1	Model construction and property prediction for amorphous materials particularly polymers.
Compass	1	A powerful molecular mechanics force field supporting simulations of solid materials.
Discover	1	molecular mechanics and dynamics methods for structure and property prediction.
Dmol	1	DMol3 - a unique density functional theory quantum mechanical code for gas phase, solvent, and solid state simulations.
Forcite	1	An advanced classical molecular mechanics tool, which allows fast energy calculations and reliable geometry optimization of molecules and periodic systems.
Polymorph Predictor	1	Polymorph Predictor - for the prediction of potential polymorphs of a given compound directly from the molecular structure.
Reflex	1	Reflex - powder diffraction simulation enhanced with indexing and refinement capabilities.
X-Cell	1	X-Cell - a novel and robust indexing program for medium- to high-quality powder diffraction data obtained from X-ray, neutron, and electron radiation sources.

Version:3.0
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all PC's at VWL and sdvlapp1 at SDVL
Categories: Chemistry, Molecular Modeling, X-ray Crystallography, Molecular Simulation

Midas Plus

The Molecular Interactive Display and Simulation (MIDAS) System is a collection of programs developed by the Computer Graphics Laboratory at UCSF. The major component of the MIDAS system is an interactive graphics display program, MidasPlus, designed for the display and manipulation of macromolecules such as proteins and nucleic acids. Several ancillary programs are also part of the system and allow for such features as computing the surface of a molecule, the selection of an active region within a molecule, computation of electrostatic charge potentials, etc. At the core of MIDAS is an unusually coherent hierarchical database system, designed specifically for macromolecules and both compact in its storage requirements and fast in its data access. MIDAS is capable of displaying molecular structures from information contained in either a Protein Data Bank (PDB) format file or a binary MIDAS database (created from a PDB file using the midas.in program). MIDAS can display molecules as line (bond) drawings, ribbons-type cartoons ("Jane Richardson drawings"), and space-filling drawings. MIDAS takes advantage of the graphics hardware available on these SGI systems to deliver high-speed display of complex molecular models. It also has virtual trackball interaction, shadow generation from multiple light sources, annotation, stereo viewing, enhanced control of van der Waals surfaces, interacctive monitoring for inter-atomic contacts during bonding and dihedral angles rotations, and direct support of MS surface files. A manual for MidasPlus is available in the Supercomputing Institute's reference library. A man page is available for MidasPlus (man midas).

Version: 2.1
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Molecular Modeling

Molden

Description

Molden is a visiualization package for viewing the molecular density, molecular orbitals, electron density, chemical structure, etc., from the output files of GAMESS, Gaussian, and MOPAC/AMPAC calculations.
With the use of the z-matrix editor initial guesses can be created for input files.

Documentation

http://www.cmbi.kun.nl/~schaft/molden/molden.html

Running

First load the Molden module
Next launch the executable

Version:3.8
Labs: IBM Power4, IBM SP, Basic Sciences Computing Lab, Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): All UNIX workstations and servers
Categories: Chemistry, Molecular Modeling

Molekel

Molekel is an advanced interactive 3D-graphics for molecular sciences It is a molecular graphics package for visualizing molecular and electronic structure data from the output of various chemistry applications (GAUSSIAN 94/98, GAMESS-US, ADF and many others.)

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the CSD package uses to access the programs and database. To do this, enter the following command:
module load molekel

Running molekel

Once you have setup your environment, use the following command to run dock
molekel

Version: 4.2
Labs: Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling, Chemistry

For on-line documentation, please visit http://www.cscs.ch/molekel/index.html.

Molmol

MolMol - MOLecule analysis and MOLecule display

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes and on-line help. The display possibilities include conventional presentations, as well as novel schematic drawings, with the option of displaying different presentations in one view. The covalent molecular structures can be modified by addition or removal of individual atoms and bonds; the three-dimensional structure can be manipulated by interactive rotation about individual dihedral angles. Special efforts were made to allow for appropriate display and analysis of sets of (typically 20-40) conformers that are conventionally used to represent the result of a NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms.

No man page is available, but program has extensive on-line help.

You must initialize your environment including default paths and environmental variables which the CSD package uses to access the programs and database. To do this, enter the following command:
module load molmol

3>Running molmol

Once you have setup your environment, use the following command to run dock
molmol

For on-line documentation, please visit http://www.mol.biol.ethz.ch/wuthrich/software/molmol/help/html/index.html.

Version: 2.1.0 SDVL & VWL, 2K.2 BSCL
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI workstations
License: Freeware
Categories: Molecular Modeling

Molscript

MolScript is a program for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures. The user supplies an input file (the script) which specifies the coordinate file, what objects to render and the exact appearance of the objects through the graphics state parameters.

Home Page

http://www.avatar.se/molscript/

Online Documentation

The on-line documentation can be found at http://www.avatar.se/molscript/doc/molscript.html.

Version: 2.1.2
Labs: Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Molecular Modeling, Image Processing

NAMD

VMD - Visual Molecular Dynamics

NAMD is a molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. For more information, see NAMD home page.

Version: 2.3
Labs: Basic Sciences Computing Lab, Origin, IBM SP, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): Origin 2000, Origin 3000, IBM SP, SUN workstations at VWL
Categories: Molecular Modeling, Molecular Simulation

O

Description (from the web page)

O is a general purpose macromolecular modelling program aimed at the field of protein crystallography. It enables the scientist to model, build and display macromolecules. O is a graphical display program built on top of a versatile database system. All molecular data is kept in this database, in a predefined datastructure. However, any data can be stored in the database. For example, data produced by associated, standalone programs can very easily be stored in the database, and used by the program, for example for colouring of atoms.
O brings into use several tools, which ease the building of models into electron density, allowing this to be done faster and more correctly. Notably, the autobuild options greatly enhance the speed of building and rebuilding molecular models. O also incorporates a graphics interpreter, allowing the user to display auxilliary 3-dimensional data, using a simple set of commands.

Home Page

http://imsb.au.dk/~mok/o/

Tutorial

http://imsb.au.dk/~mok/o/tutorial/tutorial.html

Documentation

Online at http://www.imsb.au.dk/~mok/o/o_man/manual.html (for version 5.1)
Printable postscript version in /usr/local/o/manual_5.10_letter.ps
(manual for version 7.0 not yet available)

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and database. To do this, enter the following command:
module add o
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for the CSD every time you log in.

Running O

Once you have setup your environment, use the following command to run O
o7

Version: 7.0
Labs:Scientific Development and Visualization Lab,Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Molecular Modeling, X-ray Crystallography

PROCHECK

Description

PROCHECK is a program by Roman Laskowski and coworkers which checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.

Home Page

http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

Tutorial

None

Documentation

An Online Manual is available.

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and database. To do this, enter the following command:
module add procheck
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for PROCHECK every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add procheck 
  endif
  ...

Running PROCHECK

Once you have setup your environment, use the following command to run PROCHECK
procheck

Version: v 3.4.4
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Molecular Modeling, X-ray Crystallography, NMR

PROMOTIF

Description

From the PROMOTIF documentation:

PROMOTIF provides details of the location and types of structural motifs in proteins of known structure by analysis of Brookhaven format coordinate files. The current version of the program analyses the following structural features:
Secondary structure                     Beta strands
Disulphide bridges                      Beta bulges
Beta turns                              Beta hairpins
Gamma turns                             Beta alpha beta units
Helical geometry                        Psi loops
Helical interactions                    Beta sheet topology
Main chain hydrogen bonding patterns

Home Page

http://www.biochem.ucl.ac.uk

Documentation

PROMOTIF documentation

Running PROMOTIF

First load the PROMOTIF module,

module add promotif

For a single protein use:

promotif pdb_filename

For multiple proteins use:

promotif_multi [options] input_file

see documentation for options and format details
For nmr ensembles use:

promotif_nmr [options] nmr_file

see documentation for options and format details

Version: v2.0
Labs: Basic Sciences Computing Lab
System(s): all SGI Octane workstations
Categories:NMR,X-ray Crystallography,Molecular Modeling

RasMol

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. RasMol can read in files in the following formats: pdb (Brookhaven Protein Databank), -mdl (MDL's MOL File Format), mol2 (Tripos' Sybyl MOL2 Format), xyz (MSC's XYZ format), alchemy (Alchemy File Format) and charmm (CHARMm File Format). It can display depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces. A man page is available (man rasmol), as well as on-line Reference Guide.

To use the online help from within rasmol, you must set an environment variable before you start rasmol. If you are running the csh or the tcsh, type setenv RASMOLPATH /usr/local/lib/rasmol .

Version: 2.7.1
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI and Sun workstations
Categories: Molecular Modeling

Raster3D

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, and cylinders with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in Per Kraulis' program MOLSCRIPT in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

Home Page

http://www.bmsc.washington.edu/raster3d/

Online Documentation

The on-line documentation can be found at http://www.bmsc.washington.edu/raster3d/html/raster3d.html

Version: 2.5
Labs: Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Molecular Modeling, Image Processing

Ribbons

The Ribbons software package displays molecular models as rendered images on an SGI workstation. The molecules are rendered using a ribbon representation of the secondary structure similar to a "Jane Richardson" type drawing. The data required consists of atomic coordinates in Protein Data Bank format and files of color-coding information. Version 2.0 allows the manipulation of complicated smooth shaded images in near real-time. Features include: display of multiple chains of proteins and/or nucleic acids, interactive control of the style and texture of ribbon models, color coding by a wide variety of biological and geometrical properties, display of spheres and cylinders with interceptively-set radii, display of triangular and dot surfaces, interactive control over the colors and the light source, and output suitable for use with the WaveFront ray-tracer. Hard copy documentation for ribbons is available in the Scientific Computing and Graphics Laboratory and in Workstation Room C. Documentation is in /usr/local/ribbons/doc/ribbons.ps.

Version: 2.0
Labs: Scientific Development and Visualization Lab
System(s): all SGI workstations
Categories: Molecular Modeling

SETOR

Description

SETOR is a molecular visualization package by Stephen Evens of the University of Ottawa. It is designed to display of secondary, tertiary and quaternary structures of protein and nucleic acid macromolecules, and to allow a wide variety of rendering models to be used. SETOR provides the standard methods of displaying wire-frame models of all or a subset of atoms in the molecule, but in addition can be used to generate high-quality lighted models of solid surfaces.

Home Page

http://flint.biochm.uottawa.ca/~setor_docs/

Tutorial

None

Documentation

PostScript manuals can be are found in /usr/local/setor/PostScript/.

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the program and associated files. To do this, enter the following command:
module add setor
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for SETOR every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add setor 
  endif
  ...

Running SETOR

Once you have setup your environment, use the following command to run SETOR
Setor

Version: v4.13.32
Labs: Basic Sciences Computing Lab, Scientific Development and Visualization Lab
System(s): all SGI workstations
Categories: Molecular Modeling

SPOCK

Description

from the SPOCK home page:
Spock is a full-featured molecular graphics program developed by Jon A. Christopher while in the lab of Thomas O. Baldwin of the Department of Biochemistry and Biophysics at Texas A&M University. Spock has been designed from the ground up to be powerful, flexible and most of all, easy to use. Many of the features of spock are designed to bring molecular modeling programs into the age of the internet.
Spock has the features users have come to expect from molecular graphics software including several bond and atom rendering types, and a complete array of backbone "worm" representations. Further, spock can calculate and display molecular and accessible surfaces, and color code these surfaces by properties (such as electrostatic potential).

Home Page

http://quorum.tamu.edu/spock/

Tutorial

Found in the SPOCK Manual

Documentation

Online manual found on http://www.msi.umn.edu/software/spock/Manual/Manual.html

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated fils. To do this, enter the following command:
module add spock
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for SPOCK every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add spock 
  endif
  ...

Running spock

Once you have setup your environment, use the following command to run SPOCK
spock

Version:v1.0b170
Labs: Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Molecular Modeling, X-ray Crystallography

VMD

VMD - Visual Molecular Dynamics

VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, and lipids and membranes. It recognizes many file formats, provides many types of molecule representation, 3D display and photorealistic output. For more information, see VMD home page.

Version: 1.8.3
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all UNIX workstations
Categories: Molecular Modeling

Viewmol

VIEWMOL is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results. The program s capabilities include:

Building and editing of molecules
Visualization of the geometry of a molecule
Tracing of a geometry optimization or a MD trajectory
Animation of normal vibrations or to show them as arrows
Drawing of IR, Raman, and inelastic neutron scattering spectra
Drawing of an MO energy level or density of states diagram
Drawing of basis functions, molecular orbitals, and electron densities
Display of forces acting on each atom in a certain configuration
Drawings generated by VIEWMOL can be saved as TIFF, HPGL, or PostScrip-t files
Animations of normal modes can be converted to a video file (MPEG), e. g. for inclusion into World Wide Web documents (requires additional programs available on the Internet)
Interface to the freeware ray tracing program RAYSHADE (input file genera-tion and use of RAYSHADE from within VIEWMOL)
Input and output in a variety of formats, new formats can be added easily by the user

At present VIEWMOL includes input filters for DISCOVER, DMOL, GAUSSIAN 9X, GULP, MOPAC, and TURBOMOLE outputs as well as for PDB files (VIEWMOL is therefore suited as a viewer for structural data on the World Wide Web). Struc-tures can be saved as MSI car-files, MDL files, and TURBOMOLE coordinate files. VIEWMOL s file format has been added to BABEL so that BABEL can serve as an input as well as an output filter for coordinates.

Setting up environment: module load viewmol
Documentation: /usr/local/viewmol-2.2.1/lib/viewmol/man
Examples: /usr/local/viewmol-2.2.1/lib/viewmol/examples

Version: 2.2.1
Labs: Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI and IBM systems
Categories:Chemistry, Molecular Modeling, Image Display, Image Processing

WhatCheck

Description

The WHAT_CHECK program is a free protein structure validation system written by R.W.W. Hooft as contribution to the BIOTECH protein structure validation project.

Home Page

http://www.sander.embl-heidelberg.de/whatcheck/

Documentation

An explanation of the output can be found on http://www.sander.embl-heidelberg.de/rob/checkhelp/

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated fils. To do this, enter the following command:
module add whatcheck
If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for WHAT_CHECK every time you log in.
eg:
  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add whatcheck 
  endif
  ...

Running WHAT_CHECK

Once you have setup your environment, do the following to run WHAT_CHECK

create a scratch directory and enter it using 'cd'
copy the PDB file you want to check into this directory.
run 'whatcheck' and enter the name of the PDB file when it asks you for it.
The results will be deposited into 'pdbout.txt' and 'pdbout.tex'. The first of these two is a plain text file, the second a LaTeX file. They contain the same information.

Version: 19970704-1848
Labs: Basic Sciences Computing Lab
System(s): all SGI workstations
Categories:Molecular Modeling

X-PLOR

From the X-PLOR Manual:

X-PLOR is a program system for computational structural biology. X-PLOR 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.

As long as there were no machines, programming was no problem at all; when we had a few weak computers, programming became a mild problem and now that we have gigantic computers, programming has become an equally gigantic problem. In this sense the electronic industry has not solved a single problem, it has only created them---it has created the problem of using its product. (E.W. Dijkstra, Turing Award Lecture, 1972)

X-PLOR's main focus is the three-dimensional structure determination of macromolecules using crystallographic diffraction or nuclear magnetic resonance (NMR) data. The program is based on an energy function approach: arbitrary combinations of empirical, geometric and effective energy terms describing experimental data may be used. The combined energy function can be minimized by a variety of gradient descent, simulated annealing, and conformational search procedures. The first version of X-PLOR (1.0) was published in the fall of 1987; it had evolved from a modified CRAY version of the CHARMM program (Brooks et al. 1983). X-PLOR was the first program to combine X-ray crystallographic diffraction data and molecular dynamics for refinement (Br�nger, Kuriyan, and Karplus 1987). Since then the program has undergone extensive development, and the focus has shifted from refinement to structure determination. Major features of computational X-ray crystallography and solution NMR-spectroscopy have been included. Future development of X-PLOR is aimed at providing a comprehensive system for all computational aspects of macromolecular structure determination.
X-PLOR is more than a program: it is a macromolecular language. This flexible language allows the user to experiment with new ideas without being restricted to standard or ``hard-wired" protocols. X-PLOR was designed to provide user friendliness, machine portability, and highly efficient algorithms for modern computers.

Running X-PLOR

To run X-PLOR via DQS, create a script that resembles the following:
-------------- script begins belows this line --------------
#!/bin/sh 
#$ -cwd           # output from DQS will go to the current working directory 
module load xplor # initialize xplor module 
xplor < file.inp  # run your job 
--------------- script ends above this line ----------------
Once this script is created, you can submit the job via the command:
qsub3 file.dqs
where file.dqs is your DQS script.

Version: 3.851
Labs: Basic Sciences Computing Lab,IBM SP
System(s): all workstations
Categories: Molecular Modeling

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