I am working with a protein having two binding sites, haddock works really nicely for that!! i just got the following warning: WARNING : Clustering with default parameters did not produce any cluster, cluster minimum size went from 4 to 1
so i only got one structure in the best scored cluster.
should i optimize some parameters?
thanks in advanve!
This tells you that all solutions might be rather different… I.e. no clear convergence.
Or did you change the clustering parameters?
What kind of molecules are you docking?
I did not change the parameters. I needed expert level to make a run for modelling two glycerolphosphate-multimers to one protein. for that I used docking with three molecules.
I know exactly where the binding sites are and gave exact input of interacting residues but I left the passive ones for automatical definition.
the only thing i changed after i got that warning was in the clustering paramter: RMSD as clustering method and the cutoff for the recommende 7.5 A.
is there anything else i can optimizie?
You can play with the clustering cutoff possibly.
But if your binding sites are symmetrical, better to only dock on molecule to the protein.
You will get better convergence.
Also you could try to refine your restraints.
Did you made them specific from the protein to each of your two glycerolphosphate-multimers?
Also always define the largest molecule as first one. I.e. the protein in this case I assume.
This is important if RMSD clustering is used.