I am trying to dock a monomer transporter protein with an oligomer enzyme, for example, LacY with LacZ (tetramer) or UraA with Upp (dimer). In RCSB PDB, these oligomers are downloaded in the form of biological assembly, but HADDOCK docking would rearrange these oligomer subunits. I didn’t find a way to lock the oligomer complex as the biological assembly or just merge the oligomer into a big chain. Can you help me with it? 
You have to make sure there is no overlap in numbering between your four subunits and define those as one molecule
Further if using a local HADDOCK version you should define restraints between those subunits to keep them together during the high T simulated annealing refinement stage of HADDOCK.
This can be done for example with the restrain_bodies.py script from https://github.com/haddocking/haddock-tools
If you are using the web server this is done automatically.
Thank you! A follow up question, what kind of tool would you suggest to define the subunits into one molecule?
Our pdb-tools server or local installation can do the job
Examples are provided for example in our local haddock2.4 installation tutorial available from Education & Tutorials of the Bonvin Lab – Bonvin Lab