The following software is available for use in the Molecular Modeling Center of the Department of Chemistry. Some manuals are available on the Web, as indicated. When "PDF" is noted, you will need to have the Acrobat PDF reader, or similar software, available on your computer. Other manuals are in html format.
| Program | Capabilities | Manual |
|---|---|---|
| PCModel | Molecular mechanics with MMX, MMFF, Amber force fields; simulated annealing; Monte Carlo conformation searches |
Yes - HTML |
| Spartan | Molecular mechanics with Sybyl, MMFF force fields; Monte Carlo conformation searching; semi-empirical and ab initio MO calculations; density functionals |
No - hard copy |
| Gaussian | Semi-empirical and ab initio MO calculations; density functionals | Yes - HTML |
| Gamess | Semi-empirical and ab initio MO calculations | Yes - HTML |
| Tinker | Molecular dynamics using the Charmm force field | Yes - PDF |
| Gromacs | Molecular dynamics and energy minimization | Yes - HTML |
| NAMD | Molecular dynamics with Charmm, Amber, or Gromacs force fields; parallelized | Yes - PDF |
| Modeller | Prediction of protein 2o and 3o structures based on homology | Yes -PDF |
| Autodock | Docking of small molecules to proteins and nucleic acids | Yes - PDF |
| Procheck | Analysis of protein 2o and 3o structures; Ramachandran plots | Yes -HTML | VMD | Visualize biomolecules and view MD trajectories; interact with NAMD | Yes - HTML |
| Rasmol | Visualize biomolecules from pdb files, others from Cartesians; scripting capabilities | Yes - HTML |
| gOpenMol | Visualizing MOs and molecular vibrations in Gaussian/Gamess output; visualizing MD trajectories | Yes - PDF |
| Molscript | Creates detailed Postscript pictures of protein and nucleic acid structures; script-based | Yes - HTML |