I'm new to AutoDock and I currently involved in a protein-ligand docking study. My ligand contains Cu(II) atom and a coordinated water molecule. There should be a bond between the Cu(II) atom and the O atom of the water molecule. The bond is shown when I open it using different viewer (eg. RasMol) but not in ADT. I tried to add the bond between the atoms and save it, but when I open the saved file, the bond is not add actually.
Then I tried to add the bond using Discovery Studio 3.5 Visualizer. But once I added the bond, one of the H atom of the water molecule being removed, probably because the O atom can only have 2 bonds. Can anyone tell me how to add the bond? Your help will be highly appreciated. Thanks in advance!! :)