AMBER Archive (2009)

Subject: Re: [AMBER] ptraj utility

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Dec 01 2009 - 06:56:52 CST

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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