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

From: Nhai <nhai.qn.gmail.com>
Date: Wed, 17 Jun 2015 10:04:50 -0400

Hi

Netcdf trajectory in Amber is already compressed. You don't need to zip it again (you can tell from file size before and after zipping).

So I guess cpptraj does not support zipped netcdf file for above reason.

Hai Nguyen

> On Jun 17, 2015, at 9:37 AM, Marion, Antoine <antoine.marion.tum.de> wrote:
>
> 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,
>
>
> Antoine
>
>
> ________________________________
> -- Dr. Antoine MARION
> Postdoctoral Research Scientist
>
> Department of Life Sciences
> Theoretical Chemical Biology and Protein Modelling Group
> Technische Universit√§t M√ľnchen
> Emil-Erlenmeyer-Forum 8
> D-85354 Freising-Weihenstephan
> Germany
>
> Phone: +49 (0)8161 71-2271
>
>
>
>
>
> ?
>
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Received on Wed Jun 17 2015 - 07:30:03 PDT
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