Hi,
What are the best criteria to choose the best structure from the cluster with the lowest haddock score?
Thank you
Simply the HADDOCK score I would say - which means the first model of the cluster.
But it is always good to check the other models and see how consistent they are.
Thanks.
Also, say the second model shows more number of contacts (vdw or H Bond) between ligand and the active residues of the receptor, than in the first model. Do we still consider the first model the best?
It is really up to you to choose 
Thank you