Sir,
no such experimental data other than that they form canonical wc
basepairs. i think about using it because sometimes the backbone
seems to adjusts at the penality of breaking the hbonds ( especially
terminals) .
thanking you
mary
On 11/27/14, Jason Swails <jason.swails.gmail.com> wrote:
> On Nov 25, 2014, at 2:57 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
>
> Sir,
> Is Restrained MD useful when you have a modelled dna.?
>
>
> It can be.
>
> Is it possible to give restraint to hbond between basepairs, so that
> backbone and other helical parameters adjust accordingly.
>
>
> Yes, it is possible.
>
> is it a good
> refinement approach for a modelled structure.?
>
>
> It depends. I don’t think that simple restraints preserving specific base
> pairs will really be enough to drive an otherwise-unbiased simulation to
> its native state. Also, are you
>
> getting these restraints from experimental measurements (like NOEs), or
> more empirical sources like canonical WC base pairing geometries?
> At the end of the day, I don't think just restraining a handful of
> hydrogen-bond distances will be a useful approach. You can always try it,
> though -- you may learn something from it even if, as I suspect, it doesn't
> work well.
>
> Could anyone give a sample command for the restraint.
>
>
> There is an entire chapter devoted to describing the various restraints you
> can use and how to use them
> (see chapter 23 of the Amber14 manual). That is a good place to start.
>
> HTH,
> Jason
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Nov 26 2014 - 22:00:02 PST
