Desmond Tutorial

Desmond Tutorial
Preparing a Desmond simulation with the System Builder
tein structure. Click the Preprocess button. The tables will be filled in by the Protein
Preparation Wizard.
3. Select the sodium ion in the Het table (the focus of the Workspace view will center
and zoom on the Na ion) and then click the Delete Selected button. The sodium ion is
just an artifact of the crystallization process, only the Ca ions are integral parts of the
protein.
4. You may want to experiment with H‐bond assignment as described in Figure 1.10,
but it is not essential for the current membrane setup exercise. Click the Close button
to exit from the Protein Preparation Wizard.
Figure 4.5 Preprocessing the 1su4 structure
Enter ‘1su4’ in the ‘PDB’ field
and click the ‘Import’ button.
Next, check options in this
section as shown. Do not
delete the crystal waters.
Then click the Preprocess
button.
Next, select the NA ion and
click the ‘Delete Selected’
button.
Click the ‘Close’ button.
5. Change the view to ribbon view in the Workspace and orient the protein similar to
what can be seen in Figure 4.6, which is the standard way of looking at membrane
proteins (with the transmembrane bundle aligned along the vertical axis).
48 D. E. Shaw Research September 2008