Other sources of Information

Molecular Modelling software

The following represents a brief collection of Software tools developed for Molecular modelling and visualisation. This collection focuses on the tools available at Imperial College and also on software which is predominantly free or low cost. There are of course many excellent "high-end" packages available commercially which complement the collection here, and quite a few "middle-end" packages which overlap with many of the programs noted below.
  1. Molecular Visualisation

  2. Chime Version 2.0 (Windows NT, 98 and in part Macintosh). This is a Web browser plug-in, developed in 1996 from a stand-alone program called RasMol (written by Roger A. Sayle in the early 1990s at Imperial College). It supports a wide variety of molecule coordinate formats, incouding PDB (Protein databank), Molfile (from ISIS/Draw), MOP (MOPAC input files) and GAU (Gaussian Input files). It also supports the RasMol scripting language developed by Roger Sayle, which allows complex "molecular style sheets" and animations to be developed. Other features include the display of NMR, MS, IR, UV spectra in JCAMP-DX format, and the rendering of 3D volume information in the form of Gaussian Cube files (ie molecular orbitals, surfaces etc).
  3. WebLab Viewer, an excellent commercial program with a free "lite" version, which is capable of viewing in many different modes a variety of molecular file formats.
  4. Chem3D Plugin. An alternative browser plugin to Chime. A better option if you want to use it for e.g. measuring bond distances and angles from 3D coordinates. On a Macintosh browser, you can switch between Chime and Chem3D plugins using the Edit/Preferences/Applications menu. On Windows, switching between the two is not trivial (i.e. I don't know how to do it!). Chem3D can also be used as a stand-alone program.
  5. ChemApp (all platforms supporting Java). This is an alternative to the Chime Browser plug-in. The latter is written in computer specific code, for which currently the only complete implementation is for Windows NT. Unix, Macintosh and other non-NT users have an alternative based on a language called Java, which ChemApp is implemented in. The Java is interepreted not by the operating system but the Web browser, and hence a measure of platform independence is achieved. ChemApp currently only supports CAChe files and molecular surfaces.
  6. ChemSymphony (all platforms supporting Java). Another Java-based molecular visualisation environment.
  7. MacMolPlt (Macintosh). A molecular and wavefunction visualisation program that also serves as the "front" and "rear" end for the GAMESS program.
  8. CosmoPlayer: a VRML Browser plug-in (Windows, Macintosh, SGI). VRML (Virtual Reality Modelling Language) is a recent 3D model description language, which allows complex molecular models including surfaces and schematic representations to be created.
  9. SwissPdbViewer. Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
  10. IMol, a viewing program for MacOS X.
  11. PovChem. A Ray-tracing program (Mac, Windows, Unix) that renders e.g. PDB files to superb quality. Use this for publications and reports!
  12. VEGA, a comprehensive Integrated system running on Windows and Linus. Part of the Drug Design Laboratory.
  13. Kinemage. A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared in order to better communicate ideas that depend on 3-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program called MAGE. A utility called PREKIN makes a starting kinemage from a PDB-format coordinate file which can then be modified on-screen in MAGE or off-line in any text editor.
  14. VMD: Visual Molecular Dynamics. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Unix or Windows, is distributed free of charge, and includes source code.
  15. Molecular Mechanics

  16. MacroModel 6.0/6.5 (SGI Unix).
  17. Tinker: A free suite of programs implementing a number of mechanics force fields and different optimisers. Available for Windows/Mac/Unix versions
  18. CAChe (Macintosh, Windows).
  19. Chem3D
  20. Spartan
  21. Biomer: online java applet, model builders for polynucleotides (DNA/RNA), polysaccharides and proteins, interactive molecule editor, AMBER force-field based geometry optimization, simulated annealing with molecular dynamics, and the ability to save gif, jpeg, and ppm images
  22. Ghemical is an open-source Mechanics and visualisation program.
  23. Semi-empirical Molecular Orbital

  24. MOPAC2002 (Windows, Mac). Derived from the original semi-empirical program, available for Unix systems.
  25. CAChe (Macintosh).
  26. winMOPAC (Windows 95 and NT).
  27. Spartan (Windows and Macintosh).
  28. Chem3D, implementing the MOPAC97 codes.
  29. ArgusLab 3.0: Molecular Mechanics, Semi-empirical in a package for Windows machines.
  30. Ab initio Molecular Orbital

  31. GAMESS, available for Intel Mac and Windows
  32. Dalton, Unix/Windows.
  33. Gaussian 03(G03W). The program that won its originator the 1998 Nobel prize in chemistry!
  34. Spartan
  35. Chem3D via an interface to Gaussian 03.

    Integrated Environments

  36. The Molecular Operating Environment. A very recent collection of modules for performing all modelling operations in chemistry and molecular biology
  37. iLab: Compute molecular properties on the ACD site.

  38. General Software Compilations

  39. The Computational Chemistry Archive
  40. The National Institutes of Health Software Guide
  41. Chemistry Software Collection by Rolf Claessen
  42. Linux4Chemistry: An excellent collection of Software available for Linux

[Overview|Case Studies 1-3|Case Studies 4-6|Case Studies 7-9|Case Studies 10-12|
Workshop on Transition States|Summary of available Modelling Programs]