Desmond Tutorial
Desmond Tutorial - DE Shaw Research
Desmond Tutorial - DE Shaw Research
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<strong>Desmond</strong> <strong>Tutorial</strong><br />
Preparing Free Energy Perturbation<br />
Now click Maestroʹs Adjustment tool on the left icon menu as shown in Figure 7.9 to turn<br />
on the manual adjustment option. You can click this button to switch between manual<br />
adjustment mode and global translation/rotation mode.<br />
Figure 7.9 Manual adjustment of the substitution group conformation<br />
Click the ‘Adjustment’<br />
button to enable manual<br />
adjustments, such as<br />
“quick-torsion”.<br />
Click the attachment bond (shown in green) to display the non‐bonded contacts between<br />
the butyl fragment and the ligand core. As shown in Figure 7.10, there are bad contacts<br />
(displayed in orange) and ugly contacts (displayed in red). Good contacts are not shown<br />
by default because there are too many of them. See the documentation on the Measurements<br />
panel for the Contacts tab. Removing the ugly contacts is a good idea, and the bad<br />
contacts remaining are probably not a big issue.<br />
78 D. E. Shaw Research September 2008