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 - 15:00:02 PST
