Re: [AMBER] RNA Simulation

From: Jiri Sponer <>
Date: Thu, 12 Mar 2015 20:28:48 +0100 (MET)

The first thing you need to do is secondary structure prediction
and then searching for signatures of known RNA motifs in the sequence,
such as UNCG tetraloop, sarcin-ricin loop, etc. Jiri

On Thu, 12 Mar 2015, jacob wick wrote:

> Date: Thu, 12 Mar 2015 23:58:59 +0530
> From: jacob wick <>
> Reply-To: AMBER Mailing List <>
> To:
> Subject: [AMBER] RNA Simulation
> Hi all,
> I am trying to simulate a chunk of RNA molecule (20 residues) to predict
> its tertiary structure. The crystal structure of that RNA is not available,
> so I don' t know how that chunk will finally look like.
> I am creating that 20 residues chuck by NAB and then I am simulating it for
> 100 ns as per the AMBER TUTORIAL B1 with (ht tp://
> force filed. Within few ns, I am getting a
> pseudoknot structure, after which tere is no significant change in rmsd.
> The rmsd difference between the initial structure (created by NAB) and the
> md average structure is around 52 (after re-imaging by cpptraj) which is
> constant from 5ns to rest of the simulation period.
> Please suggest what can I do to make my RNA simulation more reliable. Is
> the protocol used by me is right?
> Can I justify the huge change in the rmsd as I am starting with a streach
> created by NAB and finally I am getting a stable tertiary structure. So, as
> these two structures are quite different from each other, leads to a large
> change in the rmsd value?
> Thanks and Regards,
> Jac
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Received on Thu Mar 12 2015 - 12:30:03 PDT
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