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

From: Amparo Garcia Lopez <>
Date: Wed, 24 Oct 2012 09:58:44 +0000

Thanks very much! I tried MC-Sym and it looks very promising. At least it kind of formed a loop and gave me 4 different possible pdb's, whereas Assemble or x3DNA would only give me one and leave the loop as an ugly overhang...

I can't do programming yet, as I'm a complete beginner. So maybe trying to get this with Leap would not work in my hands..

Thanks all for your help again.
From: David A Case []
Sent: 23 October 2012 14:20
To: AMBER Mailing List
Subject: Re: [AMBER] RNA - build a mismatch and a loop with NAB

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.


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Received on Wed Oct 24 2012 - 03:00:02 PDT
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