[AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized

From: Marion, Antoine <antoine.marion.tum.de>
Date: Wed, 17 Jun 2015 13:37:47 +0000

Dear Amber community,

I am experiencing an issue while trying to read gzipped netcdf trajectories in cpptraj.

Here is the error that I get:
CPPTRAJ: Trajectory Analysis. V15.00
    ___ ___ ___ ___
     | \/ | \/ | \/ |

| Date/time: 06/17/15 15:10:01
| Available memory: 113198 MB

INPUT: Reading Input from STDIN
  [parm md.prmtop]
        Reading 'md.prmtop' as Amber Topology
  [trajin md.crd.gz]
Error: Could not determine trajectory md.crd.gz format.
Error: Could not set up input trajectory 'md.crd.gz'.
        1 errors encountered reading input.
TIME: Total execution time: 0.4719 seconds.


Notice that if I gunzip the trajectory prior to the analysis, cpptraj reads it properly.

I also tried to compress the trajectory using bzip2. The result is the same as using gzip.

I do not think that it depends on this simulation, since I get the same result with other systems.

Changing the file extension from ".crd.gz" to ".nc.gz" (as suggested in the manual) does not make the trick either.

I finally tried to specify the format in the trajin command as "trajin md.crd.gz netcdf", but I am not sure if this keyword is used at all.

Does anyone have an idea if this is a bug (or unsupported feature) or a problem coming from my files ?

Thanks in advance.

Best regards,


-- Dr. Antoine MARION
Postdoctoral Research Scientist

Department of Life Sciences
Theoretical Chemical Biology and Protein Modelling Group
Technische Universität München
Emil-Erlenmeyer-Forum 8
D-85354 Freising-Weihenstephan

Phone: +49 (0)8161 71-2271


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Received on Wed Jun 17 2015 - 07:00:03 PDT
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