ok sir,
then it would be better to allow the structure to evolve itself, adjusting
torsions and helical. isn't?
Sir, could you suggest me any criteria in arriving at a reliable structure?
may be rmsd convergence? would you prefer long simulation or multiple in
such a case?
thanking you
On Thu, Nov 27, 2014 at 5:18 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> > On Nov 27, 2014, at 12:58 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> >
> > 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) .
>
> It would be a mistake to think this is “unnatural” behavior. As I
> understand it, base pairs at the end “fray” quite frequently -- a phenomena
> that I believe has been observed and characterized experimentally. So I
> think this is a poor rationale to use these restraints, as they will
> artificially suppress the more “correct” behavior.
>
> One other thing I’ll point out about base pairings in general -- the WC
> canonical base pairs do more to confer specificity than stability (i.e.,
> mismatched bases are destabilized compared to “canonical” WC pairing, but
> the H-bonds in particular are not enough to “glue” the strands together).
> I think the Amber force field does a pretty good job of reproducing
> hydrogen bond strengths, so I would not suggest artificially increasing
> their strength through the use of restraints.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Thu Nov 27 2014 - 10:00:02 PST
