Prepare for docking with CPORT

I’m using CPORT to predict the active and passive residues for my proteins. I want to dock two subunits, one from dimer and another is from trimer. So when I use CPORT to do the prediction, should I use the dimer and trimer, or just the simple subunit? I got very different result from these two methods.
I am wondering if anyone had the same problem before.

I would use the dimer or trimer. You want to exclude from your predictions the regions that are buried in the interface between the monomers