I am trying to run on the server some docking2 tests between two known interacting proteins. In fact, I would like to explore a situation including as part of the interacting interface a ligand that is often observed in 3D structures of homologs at a site contributed by the two partners. However, when I launch jobs with ligand coordinates at its final site included in the pdb of the first partner, the simulation fails and I receive an error message.
I therefore write to ask whether any of you know a means to circumvent this obstacle.
I thank you all in advance,