Re: [AMBER] cpptraj error

From: Daniel Roe <>
Date: Tue, 14 Nov 2017 12:36:47 -0500


On Mon, Nov 13, 2017 at 6:24 AM, Rana Rehan Khalid <> wrote:
>> trajin md1.mdcrd.gz
> Reading 'md1.mdcrd.gz' as Amber Trajectory
> Warning: md1.mdcrd.gz: Number of frames in compressed traj could not be
> determined.
> Warning: Frames will be read until EOF.

This is usually due to 1) a corrupted trajectory file or 2) a mismatch
between the topology file and coordinate file (i.e. the topology has a
different number of atoms than the coordinate file). Try decompressing
the trajectory file first before reading it in; this may give you a
better idea of what's wrong. Also make sure you're using the most up
to date version of cpptraj. In the future, I recommend you save your
coordinates in the NetCDF format to avoid issues like this.

Hope this helps,


>> list
> trajin
> 0: 'md1.mdcrd.gz' is an AMBER trajectory, Parm bay.prmtop (Orthogonal
> box), unknown #frames, start=0 offset=1
> Total number of frames is unknown.
> Regards
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
AMBER mailing list
Received on Tue Nov 14 2017 - 10:00:04 PST
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