Software and Coomputers Available in the Modeling Center

 As of Fall semester 2010, we have seven computers available for the modeling class. They all are Linux boxes, running one version or another of Red Hat Linux. Three of the machines are about four years old: Kollman, Dewar, and Mulliken. The remaining four are ten years old: Coulson, Hartree, Pople, and Slater. All are named for theoretical or computational chemists and physicists. Because of their varying ages, they are running different versions of some of the software. For example, the older machines have Gaussian98 installed, whereas the newer ones have Gaussian03.

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 - PDF
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
Jmol Visualize biomolecules from pdb files, others from Cartesians; scripting capabilities Yes - HTML

This page last modified 1:11 PM on Thursday July 15th, 2010.
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