I am trying to dock a ligand (just one structure, partner 2) into an ensemble of 10 proteins structures (partner 1). I have the ten PDBs separately, then I used pdb_mkensemble to combine those, loaded into Pymol, align all states and then re-export the PDB (following the steps in the basic protein-protein docking tutorial). The distance restraints are the same. The run was completed, but the results clearly showed some error, since there is only one structure per cluster, the ligand was not correctly docked and the energies are zero (HADDOCK results page).
Important to notice that when I run HADDOCK with just one of those structures it worked great, so I am not sure what could be wrong here.
Thanks for the help!