Manual.txt

Apo-Water Dock

In the pop-up, choose the protein file (.pdbqt)

For choosing the binding site, there are two options, 
1) Either manually enter the X, Y and Z co-ordinates (in A) of the 15 A box
2) Choose the ligand file (pdb/mol2/pdbqt) that defines the binding site. WaterDock will consider the COM of the ligand as the center of the binding site. 


Holo-Water Dock

Seems straightforward. Choose the protein pdbqt file and ligand file. 
Ensure pdb/mol2 format for the ligand. pdbqt format does not include all the Hydrogens which messes up the functional group identification.