Specifying multiple ligands simultaneously

[faraguna-ginkgo]

Thanks for the repo. Is it possible to run inference on multiple ligands simultaneously (for example, a ligand and a cofactor)? Or is it possible to keep a cofactor in the protein structure that is relaxed along with the protein while another ligand is docked? I have tried --no_clean while keeping the cofactor in the protein .pdb but that results in warnings regarding an unexpected residue for the cofactor and the cofactor is removed from the output .pdb structures.