Re: [AMBER] RNA - build a mismatch and a loop with NAB

From: David A Case <>
Date: Tue, 23 Oct 2012 08:20:17 -0400

On Tue, Oct 23, 2012, Amparo Garcia Lopez wrote:
> >
> > Can I use NAB to build a stem-loop RNA with a mistmatch in the stem? I
> > tried giving NAB my RNA as single stranded, with the naive hope that it
> > would just fold it. I used this:
> > m = fd_helix ( "arna", ...)

NAB and LEaP are not well suited to this sort of task, although you could
follow the prescriptions in the "distance geometry" chapter (where a
pseudoknot is constructed.) I'd think that a program like MC-SYM would be
better suited to what you want to do.


AMBER mailing list
Received on Tue Oct 23 2012 - 05:30:03 PDT
Custom Search