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

From: Amparo Garcia Lopez <>
Date: Tue, 23 Oct 2012 08:06:39 +0000

Thanks very much Jason. What about the loop? Can I create it also with Leap? the loop is what's giving me most of the problems in all other programs I've tried, as none of them will create it. They simply don't want to close the top of the hairpin

Thanks very much again.

From: Jason Swails []
Sent: 22 October 2012 20:40
To: AMBER Mailing List
Subject: Re: [AMBER] RNA - build a mismatch and a loop with NAB

I don't think nab will create mismatches. This is easy enough to remedy
using leap, though. What you should do is generate the PDB for the
complementary sequence using NAB. Then, at the point where you want to
introduce the 'mutation' (i.e., mismatch), change the residue name to the
one that you want and delete all atoms that are not present (or have
different names) in the target residue.

LEaP will automatically add the missing atoms for you from a template. If
you end up deleting the whole base, you should do a careful minimization
and equilibration with the appropriate restraints to work your way into a
reasonable geometry.


On Mon, Oct 22, 2012 at 10:11 AM, Amparo Garcia Lopez <> wrote:

> Hi all, I apologise because this question is probably very silly, but I'm
> new to molecular modelling and to Amber, so I'm a bit (very) lost.
> 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", ...)
> and ofc what NAB did was to take my sequence and build the complementary
> strand, to produce a perfect RNA duplex. This is not what I want...
> I've tried other programs to generate a pdb with my RNA but to no
> availl... I've also read I can use NAB and do m=wc () instead, but I have
> no idea whether this will work for the loop...
> Thanks very much in advance for your ideas. In you I trust! :-)
> A.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
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Received on Tue Oct 23 2012 - 01:30:03 PDT
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