Dear Jason and Amber community members,
Thanks for the wonderful explanation.
But one doubt comes naturally to my mind.
If you are sure about the fact that isotope effect won't matter in the
phenomenon which we are trying to understand by doing MM based MD
simulations, then for what sort of applications have you considered to
include it in the coming version?
Thanks again.
On Mon, Nov 21, 2011 at 7:30 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Nov 21, 2011 at 3:27 AM, vaibhav dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Amber community members,
> > If we have protein structure data available on isotopically labelled
> > protein, can we make use of this information in AMBER and perform
> dynamics
> > with them.
> > I mean how to generate prmtop and inpcrd files with specific AA labelled
> > with 15N, 13C or 2H and try to analyze the isotopic effect for properties
> > we are interested to calculate for e.g. changes in the dyamics of a
> > particular helix or loop when it is labelled.
> >
>
> You can change the mass of those atoms in the topology file (the upcoming
> version of AmberTools will have a utility that makes such modifications
> very simple).
>
> Note though, I'm not sure how reliable of an approach this is. You will
> _never_ see EIEs via classical molecular dynamics because the equilibrium
> isotope effect is a quantum effect (indeed, the potential surface in a
> classical world is mass-independent). While you may be able to see some
> differences reflected in KIEs, I'm not sure how reliably MD reflects
> accurate time-scales for dynamics. I'd bet that hetero-atom substitutions
> (i.e. 12-13 or 14-15) will simply be lost in the noise. H-atoms are
> typically SHAKEn, so you'll probably have to turn SHAKE off (and pick a
> corresponding flexible water model for explicit solvent) if you wish to see
> deuterium substitution effects.
>
> HTH,
> Jason
>
>
> > I hope the question makes sense.
> > Thank you.
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Mon Nov 21 2011 - 08:00:03 PST
