Re: [AMBER] Reading Frames from Trajectory File

From: Daniel Roe <>
Date: Mon, 3 Feb 2020 14:12:38 -0500


On Mon, Feb 3, 2020 at 1:13 PM Catherine Jenifer Rajam Rajendran
<> wrote:
> * When I read my MDCRD file in CPPTRAJ, it shows that it's reading 18 of
> 1750 frames.
> 0: 'prod_noW.mdcrd' is an AMBER trajectory, Parm (reading
> 18 of 1750)
> Coordinate processing will occur on 18 frames.
> My mdcrd file actually contains 245,755 frames as per the following email:

Are you sure you did your math correctly here? Cpptraj bases the #
frames calculation for ASCII trajectories on the number of atoms in
the associated topology and the actual file size. The calculation
rarely fails if the topology and trajectory match.

> * When I TRAJIN my mdcrd file, I got the following warning:
> Warning: Trajectory only contains box lengths and topology has no box info.
> Warning: To set box angles for topology use the 'parmbox' command.

This is likely because the trajectory was stripped but 'nobox' was not
used, so the trajectory still contains box coordinates.

> So, apparently my topology file doesn't have box information but my
> trajectory file has box coordinates. Should I skip reading the box values
> from trajectory file? If so, Can can I do it. And, I would like to know if
> there is a way to understand why it reads less number of frames. Can
> someone help me with this?

Your trajectory contains 1750 frames. Since according to the output
you posted you're only reading in every 100th frame, you end up
reading only 18 frames.


> Thanks,
> Catherine
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Received on Mon Feb 03 2020 - 11:30:02 PST
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