AMBER Archive (2009)

Subject: Re: [AMBER] ptraj utility

From: Daniel Roe (
Date: Tue Dec 01 2009 - 06:45:19 CST

It's difficult to answer your question without some more information
about your system. I assume that since you mentioned a box this is a
periodic system, but what does your ptraj input look like, what kind of
molecule did you simulate and how big, etc.

The easiest thing for you to do would probably be to look at those
frames of the trajectory yourself using your favorite visualization
program and see if those distances make sense. Depending on your system,
it's not inconceivable that you're sampling some sort of transient event
(e.g. partial unfolding in a peptide) that is causing your distance to

Hope this helps,


Neha Bharat Gajaria wrote:
> Hi List,
> 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

Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741

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