I am trying to run on the Rosie server some docking2 tests with bound ligand in each protein. In fact, I would like to explore a situation of how two protein interacts with each other with bound ligand. However, when I launch jobs with ligand coordinates at its final site included in the PDB, the simulation fails and I receive an error message.
I, therefore, write to ask whether is it possible to do on ROSIE server?
I thank you all in advance,
Unfortunately, in order for Rosetta to recognize small molecule ligands, it needs to have an appropriate description of it. Normally this has to be manually generated.
As Rosie is intended to be a simple interface to Rosetta for the most common use cases, the protein-protein docking application on Rosie doesn't have this functionality.
You should be able to do what you're interested in with Rosetta, though you would need to use the downloaded version and not Rosie, and it may take a bit of extra effort to set things up.