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,
One of the difficulties here is that Rosetta needs parameters for the ligand you're using. The docking2 server doesn't have any facility to generate/add those parameters. (The ligand docking server is specifically written to generate those parameters for the small molecule.)
What you want to do is certainly possible with Rosetta, it's just that it requires more involvement than what the docking2 server is set up for. I'd recommend looking into running Rosetta locally, rather than on ROSIE.