Aha ! So snapshots need to be aligned first. Thanks a lot.
Regards
Mish
On Tue, Apr 10, 2012 at 8:16 PM, Gonzalo Jimenez <
gonzalojimenezoses.gmail.com> wrote:
> Dear Mish,
>
> Maybe you can try to generate an average structure first and then re-run
> ptraj again to rms your frames using that average pdb as reference. I'd bet
> that you'll obtain better b-factors (it happened the same to me)
> Good luck,,
> Gonzalo
>
> --------------------------------------------------
> From: "mish" <smncbr.gmail.com>
> Sent: Tuesday, April 10, 2012 10:55 AM
> To: "AMBER Mailing List" <amber.ambermd.org>
> Subject: [AMBER] Calculating B-factor in ptraj
>
> > Dear all,
> >
> > I am trying to calculate B-Factor of C-apha atoms by post processing
> > AMBER trajectories in ptraj. When I compute atomic fluctuation ( >
> > atomicfluct out atomfluct_CA.out .CA byres ) values varies between 18 to
> > 30 (which seems to me quite high) where as B-factor (> atomicfluct out
> > atomfluct_CA.out .CA byres bfactor) for same trajectories and same atom (
> > C-alpha) varies between 10000 to 25000; which is quite high. Values of
> > B-factors looks quite true because according to manual B-factor
> calculated
> > by multiplying the squared fluctuations by (8/3)pi**2.
> >
> > I also tried to image the trajectories ( center :1-200 mass origin ;
> image
> > center familiar com :1-200) before calculating atomic fluctuation but the
> > fluctuations remains the same. Do you think I am doing some mistake in
> > commands (mentioned above) because If I align all the trajectories in vmd
> > I
> > not see such a huge structural changed or movement of backbone atoms.
> >
> >
> > Sincerely
> > Mish
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>
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Received on Tue Apr 10 2012 - 11:30:05 PDT
