OSCompChem < GridAndHPC

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---++ Computational Chemistry

*Commercial/ Proprietary Packages*

   * Gaussian-09 vA02

*Free or Open Source*

   * GAMESS-UK - General ab initio quantum chemistry package
   * GAMESS-UK - General ab initio quantum chemistry package
   * PC-GAMESS - General ab initio quantum chemistry package
   * DALTON
   * NW-CHEM
   * Avogadro - Advanced molecular editor
   * Gabedit - Graphical user interface to computational chemistry packages
   * MOSCITO - Performs molecular dynamics simulations of rigid and/or flexible molecules
   * MPQC- Computes the properties of molecules, ab initio
   * Open Babel - Converts and manipulates chemical data files
   * !PyMOL - OpenGL molecular graphics system written in Python

*Other general Chemistry software*

   * apbs                   
     Available versions:  1.0.0-r1 ~1.2.0 {arpack blas debug doc mpi openmp python}
     Homepage:            http://apbs.sourceforge.net/                             
     Description:         Software for evaluating the electrostatic properties of nanoscale biomolecular systems                                                                                                

   * arp-warp-bin
     Available versions:  ~7.0.1-r1!f
     Homepage:            http://www.embl-hamburg.de/ARP/
     Description:         ARP/wARP is a software for improvement and interpretation of crystallographic electron density maps                                                                                   

   * avogadro
     Available versions:  ~0.9.8 ~0.9.9 ~1.0.0 {glsl python}
     Homepage:            http://avogadro.sourceforge.net/  
     Description:         Advanced molecular editor that uses Qt4 and OpenGL

   * babel
     Available versions:  ~1.6 ~1.6-r1
     Homepage:            http://smog.com/chem/babel/
     Description:         Babel is a program to interconvert file formats used in molecular modeling.

   * bodr
     Available versions:  ~6 ~8
     Homepage:            http://sourceforge.net/projects/bodr
     Description:         The Blue Obelisk Data Repository listing element and isotope properties.

   * burrow-owl
     Available versions:  ~*1.2 {examples}
     Homepage:            http://burrow-owl.sourceforge.net/
     Description:         Visualize multidimensional nuclear magnetic resonance (NMR) spectra

   * caver
     Available versions:  *0.99.2!f ~*0.99.4!f {pymol}
     Homepage:            http://viper.chemi.muni.cz/caver/
     Description:         Rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures                                  

   * chemical-mime-data
     Available versions:  0.1.94
     Homepage:            http://chemical-mime.sourceforge.net/
     Description:         A collection of data files to add support for chemical MIME types.

   * chemtool
     Available versions:  1.6.9-r1 ~1.6.10 ~1.6.11 1.6.12 {gnome kde nls}
     Homepage:            http://ruby.chemie.uni-freiburg.de/~martin/chemtool/
     Description:         A GTK program for drawing organic molecules         

   * cns
     Available versions:  *1.1!f ~*1.2!f ~*1.2-r1!f 1.2.1!f ~1.2.1-r1!f {debug openmp test}
     Homepage:            http://cns.csb.yale.edu/                                         
     Description:         Crystallography and NMR System                                   

   * coot
     Available versions:  *0.1.2!m ~*0.3.1 ~*0.3.3 **0.4_pre2-r549 {new-interface}
     Homepage:            http://www.biop.ox.ac.uk/coot/                          
     Description:         Crystallographic Object-Oriented Toolkit for model building, completion and validation                                                                                                

   * easychem
     Available versions:  ~0.6
     Homepage:            http://easychem.sourceforge.net/
     Description:         Chemical structure drawing program - focused on presentation.

   * eden
     Available versions:  *5.3 {bindist double-precision}
     Homepage:            http://www.gromacs.org/pipermail/eden-users
     Description:         A crystallographic real-space electron-density refinement and optimization program                                                                                                    

   * elem
     Available versions:  1.0.3-r1
     Homepage:            http://elem.sourceforge.net/
     Description:         periodic table of the elements

   * gamess
     Available versions:  ~20080411.1!f ~20090112.1!f 20090112.1-r1!f ~20090112.3!f {debug hardened qmmm-tinker}                                                                                                
     Homepage:            http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html                            
     Description:         A powerful quantum chemistry package                                          

   * gchemutils
     Available versions:  ~0.10.3
     Homepage:            http://www.nongnu.org/gchemutils/
     Description:         C++ classes and Gtk+-2 widgets related to chemistry

   * gelemental
     Available versions:  1.2.0 {doc}
     Homepage:            http://www.kdau.com/projects/gelemental
     Description:         a periodic table viewer that provides detailed information on the chemical elements.                                                                                                  

   * ghemical
     Available versions:  *2.01 ~2.10 ~2.95 ~2.98 {gamess mopac7 openbabel seamonkey threads toolbar}
     Homepage:            http://bioinformatics.org/ghemical/                                        
     Description:         Chemical quantum mechanics and molecular mechanics                         

   * gopenmol
     Available versions:  ~*3.00-r1
     Homepage:            http://www.csc.fi/gopenmol
     Description:         gOpenMol is a tool for the visualization and analysis of molecular structures

   * gperiodic
     Available versions:  2.0.7 2.0.10 {nls}
     Homepage:            http://www.frantz.fi/software/gperiodic.php
     Description:         Periodic table application for Linux       

   * gtk-gamess
     Available versions:  ~*2.00
     Homepage:            http://sourceforge.net/projects/gtk-gamess/
     Description:         GTK-GAMESS is a graphical frontend for GAMESS, a General Atomic and Molecular Electronic Structure System                                                                             

   * icm
     Available versions:  ~3.6.1g!f
     Homepage:            http://www.molsoft.com/icm_pro.html
     Description:         MolSoft LCC ICM Pro                

   * icm-browser
     Available versions:  ~3.6.1g!f
     Homepage:            http://www.molsoft.com/icm_browser.html
     Description:         MolSoft LCC ICM Browser                

   * jmol
     Available versions:  ~11.0.3-r1 {client-only elibc_FreeBSD vhosts}
     Homepage:            http://jmol.sourceforge.net/                 
     Description:         Jmol is a java molecular viever for 3-D chemical structures.

   * massxpert
     Available versions:  ~1.7.6 ~2.0.5 {debug doc linguas_fr}
     Homepage:            http://massxpert.org                
     Description:         A software suite to predict/analyze mass spectrometric data on (bio)polymers.

   * maxit
     Available versions:  ~*8.2
     Homepage:            http://sw-tools.pdb.org/apps/MAXIT/index.html
     Description:         An application for processing and curation of macromolecular structure data

   * molden
     Available versions:  4.4 ~4.6 4.7 {debug opengl}
     Homepage:            http://www.cmbi.kun.nl/~schaft/molden/molden.html
     Description:         Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac.

   * molmol
     Available versions:  ~2k_p2
     Homepage:            http://hugin.ethz.ch/wuthrich/software/molmol/index.html
     Description:         Publication-quality molecular visualization package     

   * molscript
     Available versions:  ~2.1.2!f
     Homepage:            http://www.avatar.se/molscript/
     Description:         Display molecular 3D structures, such as proteins, in both schematic and detailed representations.                                                                                    

   * mopac7
     Available versions:  ~1.10-r1 ~1.13 ~1.13-r1 ~1.14-r1 {debug}
     Homepage:            http://sourceforge.net/projects/mopac7/ 
     Description:         Autotooled, updated version of a powerful, fast semi-empirical package

   * mpqc
     Available versions:  2.3.1-r1 {debug doc threads tk}
     Homepage:            http://www.mpqc.org/           
     Description:         The Massively Parallel Quantum Chemistry Program

   * mustang
     Available versions:  ~3
     Homepage:            http://www.cs.mu.oz.au/~arun/mustang/
     Description:         MUltiple STructural AligNment AlGorithm.

   * openbabel
     Available versions:  2.0.2 2.2.1 ~2.2.2-r1 ~2.2.3 {doc python swig}
     Homepage:            http://openbabel.sourceforge.net/             
     Description:         interconverts file formats used in molecular modeling

   * ortep3
     Available versions:  ~*1.0.3 {debug}
     Homepage:            http://www.ornl.gov/sci/ortep/
     Description:         Thermal ellipsoid plot program for crystal structure illustrations

   * pdb2pqr
     Available versions:  1.3.0 ~1.4.0-r1 ~1.5.0 {debug doc examples opal}
     Homepage:            http://pdb2pqr.sourceforge.net/                 
     Description:         An automated pipeline for performing Poisson-Boltzmann electrostatics calculations                                                                                                    

   * platon
     Available versions:  ~*20080702!f ~20080725!f {debug}
     Homepage:            http://www.cryst.chem.uu.nl/platon/
     Description:         Versatile, SHELX-97 compatible, multipurpose crystallographic tool

   * povscript+
     Available versions:  ~*2.1.2.2.18 ~2.1.2.2.19
     Homepage:            http://www.stanford.edu/~fenn/povscript/
     Description:         Modified molscript that uses POV-Ray, does thermal ellipsoids, and more

   * probe
     Available versions:  *2.11.050121 2.12.071128
     Homepage:            http://kinemage.biochem.duke.edu/software/probe.php
     Description:         Evaluates atomic packing within or between molecules

   * psi
     Available versions:  *3.2.3 ~3.3.0 {test}
     Homepage:            http://www.psicode.org/
     Description:         Suite of ab initio quantum chemistry programs to compute various molecular properties                                                                                                 

   * pymol
     Available versions:  0.99_rc10 ~1.0-r1 1.2.1 {apbs shaders}
     Homepage:            http://pymol.sourceforge.net/         
     Description:         A Python-extensible molecular graphics system.

   * pynmr
     Available versions:  ~*0.37f
     Homepage:            http://maple.rsvs.ulaval.ca/mediawiki/index.php/PyNMR
     Description:         An NMR Extension for PyMOL, written in Python        

   * rasmol
     Available versions:  ~2.7.2.1.1-r1
     Homepage:            http://www.openrasmol.org/
     Description:         Free program that displays molecular structure.

   * raster3d
     Available versions:  *2.7c ~*2.7d ~2.7s {debug}
     Homepage:            http://www.bmsc.washington.edu/raster3d/raster3d.html
     Description:         a set of tools for generating high quality raster images of proteins or other molecules                                                                                               

   * shelx
     Available versions:  *20060317!f ~20060317-r1!f {debug dosformat openmp}
     Homepage:            http://shelx.uni-ac.gwdg.de/SHELX/                 
     Description:         Programs for crystal structure determination from single-crystal diffraction data                                                                                                     

   * sparky
     Available versions:  ~*3.113!m
     Homepage:            http://www.cgl.ucsf.edu/home/sparky/
     Description:         Graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers                                                                                      

   * validation
     Available versions:  ~*6.2
     Homepage:            http://sw-tools.pdb.org/apps/VAL/index.html
     Description:         Set of tools used by the Protein Data Base (PDB) for processing and checking structure data                                                                                           

   * viewmol
     Available versions:  ~*2.4.1
     Homepage:            http://viewmol.sourceforge.net/
     Description:         Open-source graphical front end for computational chemistry programs

   * webmo
     Available versions:
        (6.1.010)       ~*6.1.010!f
        (7.0.003)       ~*7.0.003!f
        (8.0.010)       ~8.0.010!f
        {vhosts}
     Homepage:            http://webmo.net/
     Description:         Web-based interface to computational chemistry packages

   * wxmacmolplt
     Available versions:  ~7.3 {flash}
     Homepage:            http://www.scl.ameslab.gov/MacMolPlt/
     Description:         Chemical 3D graphics program with GAMESS input builder

   * xdrawchem
     Available versions:  1.9.9
     Homepage:            http://xdrawchem.sourceforge.net/
     Description:         Molecular structure drawing program

   * xds-bin
     Available versions:  ~20080602!f {X smp}
     Homepage:            http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/
     Description:         X-ray Detector Software for processing single-crystal monochromatic diffraction data.


-- Main.RobAllan - 07 Dec 2009
Topic revision: r2 - 08 Dec 2009 - RobAllan