Thank you Drs. Case and Simmerling,
Its the periodic image in the dimeric system!
Cheers,
Neha
2009/12/1 case <case.biomaps.rutgers.edu>
> On Tue, Dec 01, 2009, Neha Bharat Gajaria wrote:
> >
> > I m trying to extract the distance between two Calpha atoms from amber
> > trajectories using ptraj. The average distance should be 10.05 Ang. After
> > 50ns or so, the distances reported in the output are very unusual.
> >
> > The output looks like
> > 9.45
> > 9.85
> > .
> > .
> > .
> > 40.23
> > 33.12
> >
> > .
> > .
> > .
> > 8.10
> > 8.93
> >
> > Are some of the trajectories corrupted or something is going wrong with
> the
> > box? thanking you for your response
>
> If the two CA atoms are in the same polypeptide chain, then it should not
> be
> an artifact. Visualize the trajectory and see what happens at the time
> steps
> when the distance is large. If the two CA atoms are in different
> molecules,
> it could be imaging problem...use the image command in ptraj to bring
> everything back to the main unit cell before issuing the distance command.
>
> ...dac
>
>
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>
--
Regards,
Neha Gandhi Gajaria,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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Received on Tue Dec 01 2009 - 18:30:02 PST
