Desmond Tutorial

Desmond Tutorial
Tutorial Steps
Figure 1.6 Changing from ribbon to ball-and-stick view
Double-click the
‘Draw Atoms in Ball
and Stick’ icon.
Click the ‘Color By
Elements’ button.
Once you have arrived at this point, you are ready to prepare the structure for simulation.
Just having a molecular model in the workspace is not enough to perform molecular
mechanics/dynamics calculations. You must prepare the protein model so that it
corresponds as closely as possible to the biological system you are studying.
From this view, it is clear that there are no hydrogen atoms in the protein structure.
Moreover, there might be ill‐defined bond orders, protonation states, formal charges,
tautomerization states, disulfide bonds, and so on. The red dots shown in the workspace
represent crystal waters. All of these issues must be resolved before we can perform
simulation calculations.
There are two methods of correcting these issues: the Build Panel opens Maestroʹs
general purpose molecular structure editor and the Protein Preparation Wizard is a
very useful, automated tool for protein structure preparation. For this tutorial, we will
use the Protein Preparation Wizard.
9. Select Workflows > Protein Preparation Wizard from the menu bar.
The Protein Preparation Wizard appears as shown in Figure 1.7.
September 2008 D. E. Shaw Research 7