Is it possible to coax rosetta to dock, say, a predefined dimer or trimer of small molecules to presumed binding site ona protein ? Rigid body ligand is OK.
Rosetta doesn't have any particular filters for the chemical reasonableness of the ligands it docks. (This is taken advantage of with enzyme design, where non-physical transition state hybrids are often used.)
As such, you can certainly make a single "ligand" out of an agglomeration of multiple other ligands. The only caveat is that (for technical reasons) the residue must be fully connected. You'll have to add some sort of bond between the various ligands. (Rosetta does have support for pseudo bonds, but the input formats to molfile_to_params may or may not. ) The upshot is that there's no check on the Rosetta side whether that bond is chemically feasible -- it can be at an odd geometry and/or distance and be fine. Just so long as there's a continous connection between the various sub ligands.