Hello,
Currently I am trying to do water refinement of protein - ligand complexes I calculated with CYANA.
For this, I was wondering why HADDOCK web portal does not need any distance restraint inputs whereas for example the cns software accepts the restraints as input?
Thanks a lot in advance!
The refinement interface is a simple interface not allowing the definition of any restraints.
If you want to add restraints, you can do so via the regular submission interface following the following recipe to set up a refinement run:
But for the restraints section, provide your restraint (in CNS format) as unambiguous (or ambig if you want to allow for the default 50% random removal)
Thanks a lot for the fast answer!
The param file + input section of the submit file section is temporarily disabled and forwards me to the normal submission.
Do I always need to provide 2 separate pdb files (ligand and protein) for the normal submission or does it also accept the complex structure?
You do need to provide those separately for the regular interface
Hi there, docking and refinement are different protocols.
Docking: the goal is to “put molecules together” and for that you can use restraints to guide the spatial search and scoring.
Refinement: the interacting partners are expected to already be in a complex conformation and then both will be refined - without any spatial search, hence no need for restraints.
In our web platform I have made a interface that you can input your complex as one structure (each molecule in a different chain) - which follow the same steps of the advanced refinement (so you don’t need to click so many buttons 
)
However if you have a specific case or if the restraint energy term is relevant to your study case, it’s recomended that you follow the advanced refinement guide and tweak it to your needs.
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