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Modeling Heme Proteins using InsightII and CHARMm

The purpose of this workshop is to acquaint you with the basics of molecular modeling and what is needed to perform modeling using the InsightII interface. The example we will be using is the Cytochrome C protein (entry 5cyt.pdb in the Brookhaven Protein Data Bank)

During this hands-on workshop you will:
  • learn to "read" a PDB file;
  • study different types of forcefields;
  • learn what a simulation engine is;
  • prepare your system for molecular dynamics;
  • do minimization for your system;
  • set up a molecular dynamics run;
  • read the results of a short MD run and display them