Thanks for the reply.
The behavior of ptraj with compressed files is observed with other
trajectory files as well. I even tried to decompress and recompress the file
again to see if this will eliminate the problem; but it did not.
I should say that with another version of Ambertools, installed on a linux
server, I don't see such behavior!. Is the problem related to that
particular version (1.3) or to how it was compiled (using gcc 4.01 and "-g95
option")? I'm not sure! But the compilation went through successfully
without a problem, apart from the failed test mentioned in the previous
e-mail.
I'm still puzzled with ptraj's behavior when reading the .gz file.
Any suggestion to solve this problem is very much appreciated.
Many thanks,
Ibrahim
On 4/12/10 8:12 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> On Fri, Apr 9, 2010 at 7:14 PM, Ibrahim Moustafa <I.moustafa.psu.edu> wrote:
>
>>
>> Is there a way to tell ptraj that the file is a trajectory "gzipped" file
>> more than the extension mdcrd.gz?!!
>>
>
> Ptraj should be able to differentiate between trajectories and restart
> files, even when they are compressed. If I run ptraj with input similar to
> yours I see this in my output:
>
> PTRAJ: trajin strip.run0.crd.gz 400 500 1
> Checking coordinates: strip.run0.crd.gz
> idFilesig: Gzipped file
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: strip.run0.crd.gz
> If this is not a compressed file then there is a problem
> Rank: 0 Atoms: 4049 FrameSize: 98391 TitleSize: 30 NumBox: 0 Seekable 0
>
> The fact that you're able to process your trajectory when it is uncompressed
> is strange. Does this behavior happen with any other compressed trajectories
> you have or is it just this one? If possible, could you provide me with the
> topology file and trajectory you are using? Thanks!
>
> -Dan
>
>
>> Thanks for help,
>> Ibrahim
>>
>>
>> On 4/9/10 7:02 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>>
>>> On Fri, Apr 9, 2010 at 6:40 PM, Ibrahim Moustafa <I.moustafa.psu.edu>
>> wrote:
>>>> Dear all,
>>>>
>>>> I managed to install AmberTools 1.3 on my Mac Osx 10.4 PPC following
>> the
>>>> installation guide and after using ³-g95² option.
>>>> Also, I applied the ³bugfixall² after installation. However, I ran
>> through
>>>> two issues:-
>>>>
>>>> 1) In doing the test the following did not pass
>>>> -----------------------------------------------------------
>>>>> Running test to do simple lmod optimization
>>>>
>>>> 1c1
>>>> < Glob. min. E = -128.257 kcal/mol
>>>> ---
>>>>> Glob. min. E = -135.830 kcal/mol
>>>> FAILED (probably OK if energy is -120 to -130)
>>>> ---------------------------------------------------------------
>>>> Q: Is that usual to see such a difference in the test?
>>>>
>>>> 2) The ptraj is unable to read the .gz trajectory file. However, it
>> works Ok
>>>> with the unzipped file.
>>>> I get the following error message in the case of .mdcd.gz file
>>>>
>>>>
>> ----------------------------------------------------------------------------
>>>> ---------------------------------
>>>>> readAmberRestart(): sscanf on atoms and time in restart file
>>>> filename.mdcrd.gz failed
>>>>
>> ----------------------------------------------------------------------------
>>>> -----------------------------------
>>>>
>>>> Q: Has anybody come across this before? Any suggestion to solve this
>>>> problem. It is more convenient to deal with the .gz rather than the
>> unzipped
>>>> file.
>>>
>>> True, but it is even more convenient to deal with netcdf rather than
>>> even a gzipped mdcrd. However, on to the problem:
>>>
>>> The error message tells you that it's trying to open that file as a
>>> restart, which is not what you want. What does your ptraj script look
>>> like?
>>>
>>> If it tries to open the file as a gzipped mdcrd, then it should work
>> fine...
>>>
>>> Good luck!
>>> Jason
>>>
>>>>
>>>> Many thanks in advance for your help.
>>>>
>>>> Thanks,
>>>> Ibrahim
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>
>>
>>
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>
>
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Received on Mon Apr 12 2010 - 07:00:02 PDT
