Question: How To Add Bond Between Metal Atom And Coordinated Water Molecule?
0
gravatar for Alyse
6.5 years ago by
Alyse0
Alyse0 wrote:

Hi everyone,

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!! :)

• 2.5k views
ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Alyse0

this is a highly specialized question that you should probably ask on the AutoDock forums

ADD REPLYlink modified 6.5 years ago • written 6.5 years ago by Istvan Albert ♦♦ 79k
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