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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Nov 21 2011 - 06:30:02 PST
