quick question: how do deal with HIE residue in my protein when performing the refinement stage? The web server does not recognize HIE as HISE. Any help in this?
The server only accepts HIS and will automatically defined the protonation state using molprobity
I you want to define those manually, you would have to use the guru interface and change all settings to those used by the refinement server (save a parameter file and look at the changes compared to a default docking using the easy interface.
Then, when submitting an ensemble of structures, does HADDOCK refinement stage match the corresponding protein-peptide partner? I mean, in protein.pdb and in peptide.pdb, I will put 20 structure respectively, which are from 20 complexes.
Yes - the matching is one to one in the refinement interface, e.g. model 10 in your protein ensemble will be combined with model 10 in your peptide ensemble.