Dear Dr. Francesco and Amber community members,
Thank you for highlighting these applications. I will surely go through
them and try to learn and make use in my work in the future.
On Mon, Nov 21, 2011 at 9:48 PM, Francesco Paesani <fpaesani.ucsd.edu>wrote:
> 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
>
>
> _______________________________________________
> 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 - 09:00:02 PST
