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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Received on Sat Mar 30 2013 - 09:30:02 PDT
