Hi Vaibhav,
You can actually study isotope effects with Amber using path-integral molecular dynamics, PIMD (see chapter 5 of the manual). You can also study KIE by combining PIMD and similar approaches with reactive "force fields" or QM/MM (see section 5.6 of the manual). We have studied quantum effects on both thermodynamic and kinetic properties of condensed phase systems using the methodologies described in the manual, eg: J. Phys. Chem. B 113, 5702 (2009), J. Chem. Theory Comp. 6, 2566 (2010).
I hope this can help.
Best wishes,
Francesco
----------------------------------------------------------------------
Francesco Paesani, Ph.D.
Assistant Professor
Department of Chemistry & Biochemistry
University of California, San Diego
Urey Hall 3242
9500 Gilman Drive #0314
La Jolla, CA 92093-0314
phone: (858) 822 - 3383
email: fpaesani.ucsd.edu
web: http://paesanigroup.ucsd.edu
----------------------------------------------------------------------
On Nov 21, 2011, at 7:34 AM, vaibhav dixit wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Nov 21 2011 - 08:30:06 PST
