RNA Parameter File

This ends up being a little tricky.

The "STEM" lines define constraint energies that help guide residues towards each other such that they form Watson-Crick type geometries. They also do one more thing -- if you have multiple chains (you can define the boundaries with the "CUTPOINT_OPEN" tag), the n chains will be connected across n-1 residue pairs using Watson-Crick geometries drawn from a crystallographic model of the large ribosomal subunit.

You can force a noncanonical pairing by:

OBLIGATE PAIR 10 32 W H A

The obligate forces a rigid body connection between the residues; it will be drawn at random from W/H pairs the ribosome in this case. If the residues 10 and 32 are one different strands, e.g., suppose you have a line like:

CUTPOINT_OPEN 15

then you're fine. Otherwise, the code will pick a random place to break the chain between 10 and 32, and use an energy term to try to keep the chainbreak as small as possible during folding. If you want to specify this chainbreak location (instead of it being random), you can use a CUTPOINT_CLOSED line.

Finally, the A/P specification is a different classification than the Leontis/Westhof cis/trans classification; it is based on the angle between base normals, and I found this more intuitive. Basically, if you assume the nucleobases are attached to the backbone by anti- chi angles (the "usual" glycosidic angles for RNA), A or P means the backbones are going antiparallel or parallel, respectively. [In the future, we should probably put in cis/trans as an option for specification as well.]

Hope that helps.

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!

I've let Rhiju know you've asked. The forum software was rebooted since this was done originally, (so all the accounts were wiped), so it may be a while before he gets back to you.

Rhiju says:

For G*U wobble pairs, you can use STEM PAIR; it is considered a Watson-Crick pair by the code.

We haven't included cis/trans classifications yet, because the code authors find antiparallel/parallel more intuitive and robust from a modeling perspective. Given a set of interacting base edges, there is a mapping from cis/trans to parallel/antiparallel, however, and allowing cis/trans input would be a good feature for future updates of Rosetta.