Setup for protein dock to protein homodimer

[amjjbonvin]

Hi Han

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

Dealing with dimers

Hellow everybody I have problems using Haddock for dimers. I’ve received several different messages: Using pdb (from pdb databse) There was an inconsistency in your data Error message First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble using a pdb with only one chain (but is a dimer) There was an inconsistency in your data Error message First pdb file contai…

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.