Many thanks for your reply!
I will definitely go through the paper references suggested by Jiri.
Best,
Jac
On Fri, Mar 13, 2015 at 2:45 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> And you might want to try a few starting structures. In general one might
> not see movement from one folded structure to another in reasonable
> execution times.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: Jiri Sponer <
> sponer.ncbr.muni.cz> </div><div>Date:03/12/2015 12:28 PM (GMT-08:00)
> </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject:
> Re: [AMBER] RNA Simulation </div><div>
> </div>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 <jacobwick.la.gmail.com>
> > Reply-To: AMBER Mailing List <amber.ambermd.org>
> > To: amber.ambermd.org
> > 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 all_nuc94_ol_bsc0.in (ht tp://
> > fch.upol.cz/en/rna_chi_ol/) 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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> >
>
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Received on Thu Mar 12 2015 - 22:30:02 PDT
