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

From: M. L. Dodson <>
Date: Tue, 23 Oct 2012 07:31:59 -0500

On Oct 23, 2012, at 3:06 AM, Amparo Garcia Lopez wrote:

> 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.
> Amparo

Excuse me for inserting myself into this dialog, but the AmberTools manuals
(at least as far back as I can remember) have always had an example program
for creating RNA pseudoknots. See page 450 of the AmberTools12 manual.

This is definitely not an entry level nab project, but if you know the key
distances that define the structure you want to create, then this approach
may well do what you want (to within the capabilities of the force fields
available in nab.) The program itself contains the pseudoknot distance
restraints, so would not be appropriate for you use as given. Programming
will be required.

Bud Dodson

> ________________________________________
> 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.
> HTH,
> Jason
> 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
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
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Received on Tue Oct 23 2012 - 06:00:02 PDT
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