The purpose of this workshop is to acquaint you with the basics of molecular modeling and what is needed to perform modeling. The example we will be using is the DNA binding domain of the Estrogen Receptor (entry 1HCQ.pdb in the Brookhaven Protein Data Bank).

During this workshop you will learn about:

• forcefields - what are they, what types of forcefields exist, what are the topology and parameter files in CHARMm22 forcefield;
• simulation engines - NAMD2, CHARMm, Discover,etc;
• preparing a system for simulation and verifying it - loading a PDB file from the Protein Data Bank, preparing the PDB file for the program you want to use, fixing bonds, replacing residues, adding hydrogen bonds, assigning charges, reading your PSF file and visualizing your system in VMD;
• setting up minimization, equilibration and dynamics for a system using NAMD2;
• visualizing and analyzing the results of your simulation;
• presenting your resluts through pictures