Desmond Tutorial

Desmond Tutorial
Preparing a Desmond simulation with the System Builder
Figure 4.8 Selecting the excluded region
Click the ‘Molecule’ tab,
select ‘Molecule type’,
and select the CA ions.
Click the ‘Proximity’
button and set the
distance.
8. Select the two calcium ions by “molecule type” and use the Proximity button to select
all residues within 5 Å. The resulting ASL expression at the bottom of the selection
window defines the excluded region. Click the OK button.
9. Click the Candidates button in the Advanced ion placement window shown in
Figure 4.7. A list of all negatively charged residues, which lie outside of the excluded
region appear in the table as shown in Figure 4.9.
Figure 4.9 Placement of the counterions
Use Shift-Click to
select the first 23
residues.
Click OK.
Note that the 1su4 structure has a net total charge of –23 after being processed with
the Protein Preparation Wizard. The candidate residues are listed in the table in no
particular order; therefore, if you select the first 23 residues, a good spacial distribution
of the positive counterions should result. Click the OK button.
10. Temporarily turn off the ribbon view so you can see the visual feedback of candidate
selection in the Workspace. The 1su4 structure should appear similar to the Workspace
in Figure 4.10.
50 D. E. Shaw Research September 2008