I recently read in the manual that "partners" parameter must be set in the order of how they are set in the PDB. However, I was unaware of this previously and set my partners as LH_A, while my pdb files are ordered as HLA. The docking is working and has been running for a couple days, but I am wondering if this will affect the results of the docking?
I haven't looked at the code, so I can't say for certain, but from what I recall the chains on each side of the underscore are usually treated as a set, so if you have HL_A versus LH_A likely doesn't make too much difference (the H and L chains are treated as a joint unit). If you're not getting crashes and your results are looking good, I'm guessing you're fine. (Though I'd try to match things up for future runs, just to be safe.)