Member Site Forums Rosetta 3 Rosetta 3 – General RNA Parameter File Reply To: RNA Parameter File


    I know it has been a few months since this topic was discussed, but I have a related question. For a GU Wobble pair, since the bonds are between the Watson-Crick faces of each, would I use the “STEM PAIR” tag or the “OBLIGATE PAIR” tag? Or does it make a difference?

    I would also enjoy seeing a cis/trans specification, since this is gaining more popularity :)

    Thank you!