I am trying to create a RNA aptamer ligand complex. What commands in Rosetta would you use to create a RNA structure with a ligand bound at a specific site? How would you create such a fasta file and parameter file, or is it even possible to do so in Rosetta?
As shipped, Rosetta3.1 is not compatible with what you want to do. It's ultimately possible but it requires somewhere between a lot and a huge amount of fiddling with it.
It's not clear to me what you mean by "Create a complex" - do you mean you want to do small molecule ligand docking against an RNA rather than a protein? If you just want a mental model you can just do it manually in PyMOL...
Yes, I want to do small ligand docking agaisnt an RNA instead of protien. Is that possilbe in Rosetta?
It might be possible, but it might take a lot of work. As a first attempt, you need to go into the rosetta database, find the RNA parameter files and patches, and port them over into the fullatom residue type set. You might want to replace the DNA files with the RNA files if you have no DNA in your system. Once you've done that, you should be able to read RNA structures into the ligand docking application - I'm sure there will be pitfalls after that but I'm not sure where they'll be...