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.

-- RobAllan - 07 Dec 2009