CenteroidFold and RNAfold (would the presence of FMN make a difference?)

I was running some of the designs through CenteroidFold and RNAfold mentioned at…, and the result were very different from the 2nd state for both of the labs I tested. How much of a difference does that aptamar and the FMN molecule make?

Also, I saw some weird things like a loop with a single G on one side and *7* bases on the other side. Seems like there is something major missing from the EteRNA simulation.

I don’t know about CentroidFold, but with RNAfold, I typically approach the problem of conformational changes (like switches), by using constrained folds (option -C for the command line).