In this section, you will download a file from the Protein Data Bank and perform some simple molecular mechanics calculations.

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Go to PDB workbench
1. In the search window (in the blue bar), type in: 1OMB (that's an "oh") and click the "Site Search" button. The 1OMB code is the Protein Data Bank ID for a small protein found in funnel web spider venom. (NOTE: You can use the search window to find files for all sorts of different proteins).

2. Near the upper left of the screen, click Download Files, then click on PDB File. Save the file at a convenient location on your computer.

Go to WebMO workbench
3. Use the guest account (username: guest, password: guest) to log in the WebMO demo site.
Click New Job -> Open Editor. A small window opens where you build molecules.

4. In the WebMO Job Manager Window, choose New Job -> Create New Job.

5. Now click Import Molecule. In the Import Molecule window, click the Format pulldown menu and choose PDB Format. Click the Generate Bonds box, then Browse to the location of the 1OMB file you downloaded and double click on the file. You may need to drag on the corner of the Import Molecule window to increase the window size.
Near the bottom of the Import Molecule window, click the Import Molecule button.

Experimental Xray data of proteins contain water molecules, and often do NOT have all of the H atoms present in the structure since their positions are not always determined experimentally. There may be other problems with downloaded structures (missing protein side chains, etc.). This structure has all H's in place and no missing side chains.

6. Click on the blue Continue button, choose Tinker as the engine, then Type in/Choose the following:
Job Name: (Use an appropriate name of your choice), Calculation: Geometry Optimization, Force Field: OPLS/AA

7. Click the blue Continue arrow. Your job should appear in the queue. When the job is complete, click the filename to view, etc., as before.