Setup for protein dock to protein homodimer

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to

Does anybody know how to setup protein to dock a protein homodimer.
Since there are two chains in a homodimer (A subunit and B subunit), how can I assign
the residues in A subunit and/or in B subunit. What is the format I should use.
Please let me know.

Thank you,


Hi Han

There are quite a few answers already to that question in our forum (which is by the way searchable). E.g.:

In short you need to renumber the second monomer to avoid overlap in residue number and give it to HADDOCK as a single chain PDB.