Incorrect docking results

I am trying to dock an protein and peptide. When I had the basic version I docked without restraints (only active/passive) and it worked.
but when I was upgraded to GURU and used restraints, the docking score became -1.2 and in the PDB file I see them very far apart.
What can cause this?
project ID 226078

Wrong restraints?

How did you create those? Did you specify the correct chainIDs?

I found them using NOESY spectrum,
example for a restraint I used is
assign(segid A and resid 24 and name HD)(segid B and resid 3 and name HG*) 3.5 2.0 2.5
and I used the correct chain ID, any ideas?

By default all non polar hydrogens are deleted… :slight_smile:

You can turn off that option in the distance restraint menu

And make sure the naming of your protons in that case correspond to the naming used by HADDOCK.