Docking of a nanobody and antigen without knowledge of the active sites of the proteins

How do I dock two proteins that I don’t know their active or passive sites? Thank you

You can use the ab-initio mode of HADDOCK (center of mass restraints or random AIRs), and will need to increase the sampling to e.g. 10000/400/400 for the number of models.

Or try some other docking software/server like cluspro for example