Desmond Tutorial

Desmond Tutorial
Desmond Tutorial
Figure 1.7 Protein Preparation Wizard
Check these options:
– ‘Assign bond orders’
– ‘Add hydrogens’
– ‘Treat metals’
– ‘Delete waters’ (set the
distance to a small value
to remove all water
molecules)
Click the ‘Preprocess’
button.
10. In the Preprocess and analyze structure section, check these options:
— Assign bond orders
NOTE
— Add hydrogens
— Cap termini. Set this option if you want the N or C termini capped. There are
many capping groups available; the most common are ACE on the N terminus
and NMA on the C terminus.
— Detect disulfide bonds. The 4pti structure has three disulfide bonds, which are all
correctly recognized by the Protein Preparation Wizard.
— Delete waters. Set this option if you have a reason to remove crystal waters. Set
the distance to a small value to remove all water molecules. “Het groups” refers
to atoms that are labeled HETATM in a PDB file (anything that is not a protein
residue or water).
In most cases crystal waters should not be removed from the interior of the protein molecule,
or near the protein surface. These water molecules are crucial structural components
of the protein and cannot be adequately reproduced by the algorithm used to
solvate the system later on.
8 D. E. Shaw Research September 2008