I’ve now tried to run the docking but I’m having issues with the actual sugar tree itself. The first NAG - Asn bond seems to be in place but after that the other residues in the sugar tree just seem to completely be blown out from their original position despite the fact that they were covalently bonded. The exact sequence of my sugar tree is NAG-NAG-BMA-MAN-NAG-MAN so I know the residues should be supported. I think this issue was addressed before:
however, in the thread it was mentioned that HADDOCK now supports glycosylated proteins. My assumption then was that I didn’t need to do anything since HADDOCK would automatically recognize the sugar tree. So I’m wondering if I need to now restrain the sugar tree as a ligand and whether or not I need to name all the residues as something common i.e. not have differently named residues like NAG/BMA etc. Then I use ligand restraints to maintain the sugar tree.
I should lastly also add that I added the sugar tree in silico using glyprot since the actual structure hasn’t been solved before for this case. I don’t think that should make a difference but I thought it was worth mentioning in case I’m doing something else.