Since I can't reproduce the bug with the compressed trajectories I have it's
difficult for me to figure out what might be going wrong. If possible, could
you provide me with the topology file and trajectory you are using? If the
trajectory is too big you could use ptraj on the uncompressed trajectory to
just give me a few frames. Thanks!
-Dan
On Mon, Apr 12, 2010 at 9:39 AM, Ibrahim Moustafa <I.moustafa.psu.edu>wrote:
> 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
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Mon Apr 12 2010 - 08:30:06 PDT
