Hi,
At this point it is difficult to diagnose the issue without more
information. Could you send me the complete ptraj/cpptraj output
(stdout and stderr) that you get when you attempt to run with the
unzipped files? If you are running ptraj put 'prnlev 5' at the
beginning of the script to enable debugging info (for cpptraj the
command is 'debug 5'). Also, let me know the version of AmberTools you
are using and whether any bugfixes have been applied.
Additionally, if the trajectory file is not too large you could send
me (off-list) that and the corresponding topology file, and I can try
to debug from my end.
-Dan
On Thu, Jul 12, 2012 at 11:39 PM, Catein Catherine
<askamber23.hotmail.com> wrote:
>
> Dear Dan,
> Thanks. I tried too. But unzip files also cannot be run. Any potential sources of problem?
> Annie
>
>> Date: Thu, 12 Jul 2012 23:05:24 -0600
>> From: daniel.r.roe.gmail.com
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] How to read netcdf files to ptraj?
>>
>> Hi,
>>
>> On Thu, Jul 12, 2012 at 10:54 PM, Catein Catherine
>> > Error: Could not set up file ../test.netcdf.gz for reading.Error: trajin: Could not set up trajectory.
>>
>> Compressed Netcdf files are not supported - there should have been an
>> error or a warning message written stating this. You should decompress
>> the gzipped Netcdf file before trying to process it.
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Lab Specialist
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Jul 13 2012 - 07:30:03 PDT
