Thanks a lot for the response...i read the article you mentioned.
I have used Amber12 force field ff12SB (with OL3 corrections) for all my
simulations (effect of different force fields on RNA systems has been
documented in your recent articles).
As i mentioned that my systems are mutants of the original crystal
structure, how can we suggest whether any conformational difference
observed is a result of force field limitations or is an actual consequence
of mutations. (Though, all recent papers recommend ff12SB with OL3)
I am a bit confused in this regard....
Thanks
Asmita
On Sat, Mar 30, 2013 at 9:41 PM, Jiri Sponer <sponer.ncbr.muni.cz> wrote:
> This is not easy question.
> 2.3 A could be more or less good start structure.
> Modifications make a sense, MD should capture their
> effect.
> It depends if they are isosteric or not.
> However, if and when to see changes, it is case by case.
> With increasing the simulation time, the probability
> to see something increases, but also to see force field
> problems.....
>
> I would tell multiple 100-500 ns simulations are good
> option.
>
> Look at this papar where we tried to see similar issues,
> expanding in some cases above microseconds.
> Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics
> Study
> Author(s): Banas, Pavel; Sklenovsky, Petr; Wedekind, Joseph E.; et al.
> Source: JOURNAL OF PHYSICAL CHEMISTRY B Volume: 116 Issue: 42 Pages:
> 12721-12734 DOI: 10.1021/jp309230v Published: OCT 25 2012
>
> Note that RMSd is a poor descriptor, it tells nothing, you must analyze
> the details of the structure.
>
>
> Best wishes, Jiri
>
>
>
> On Sat, 30 Mar 2013, Asmita Gupta wrote:
>
> > Date: Sat, 30 Mar 2013 21:14:39 +0530
> > From: Asmita Gupta <asmita4des.gmail.com>
> > Reply-To: AMBER Mailing List <amber.ambermd.org>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: [AMBER] conformational sampling in non helical RNA structures
> >
> > Dear Users,
> >
> > I am running an MD simulation on an RNA aptamer, (2.3 Ang resolution, 20
> > residues). Apart from the native state, i have generated 3 mutant forms
> of
> > the original crystal structure. These mutations correspond to either
> single
> > base mutations or base pair substitutions.
> >
> > As i am not sure about the behaviour of these mutant forms, current
> > simulation time is limited to 100ns. I don't know whether extending the
> > simulation time will bring the system to convergence or the system will
> > fall apart.
> >
> > My purpose is to generate a set of ensembles for analysis of
> > conformational differences in mutant forms. Can you please suggest what
> > should be done to enhance sampling. Is extending the time scale is a
> viable
> > solution(in case of above uncertainty)
> >
> > I calculated RMSD for all heavy atoms. The curve was stable after 70ns,
> > but RMSD for the loops seemed to increase after 90ns.
> >
> > Thanks
> >
> > Asmita
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Sat Mar 30 2013 - 11:30:03 PDT
