I can confirm this bug. Appears to be a problem with compressed trajectories
- if I decompress the trajectory first it works fine. Looking into the bug
now...
-Dan
On Fri, Apr 16, 2010 at 3:53 PM, Tom Joseph <ttjoseph.gmail.com> wrote:
> Apologies in advance for the probable silliness of this question, but
> with the 14 Apr release candidate of AmberTools (compiled with
> "-nobintraj -noX11 -nosleap gnu"), the following ptraj commands do not
> generate an average structure in foo.pdb, whereas they do with the
> AMBER 10-era ptraj:
>
> trajin md5.trj.gz
> average foo.pdb
> go
>
> ...where md5.trj.gz is a gzipped mdcrd trajectory. It isn't clear to
> me from the documentation in CVS (or else I missed it) how my commands
> are incorrect. I have the same (lack of) result with CVS AMBER 11's
> AmberTools. The ptraj output is below.
>
> Thanks,
> --Tom
>
> $ $AMBERHOME/bin/ptraj solute.pdb
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 11.0 integrated" (4/2010)
> -/- Executable is: "/home/josept02/build/14apr10/amber11/bin/ptraj"
> /-\ Running on 1 processor(s)
> \-/ Reading PDB file "solute.pdb": 12004 atoms found!!!
> Found 720 residues
>
> PTRAJ: Processing input from "STDIN" ...
> trajin md5.trj.gz
>
> PTRAJ: trajin md5.trj.gz
> Checking coordinates: md5.trj.gz
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: md5.trj.gz
> If this is not a compressed file then there is a problem
> Rank: 0 Atoms: 12004 FrameSize: 291723 TitleSize: 81 NumBox: 3 Seekable 0
>
> average foo.pdb pdb
>
> PTRAJ: average foo.pdb pdb
> Mask [*] represents 12004 atoms
> go
> [No output trajectory specified (trajout)]
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur until EOF (unknown number of
> frames).
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (md5.trj.gz) is an AMBER trajectory (with box info)
> NO OUTPUT COORDINATE FILE WAS SPECIFIED
>
> ACTIONS
> 1> AVERAGE: dumping the average of the coordinates to file foo.pdb
> start: 1 Stop [at final frame] Offset: 1
> Atom selection * (All atoms are selected)
> Output file information: File (foo.pdb) is a PDB file
>
>
> Processing AMBER trajectory file md5.trj.gz
>
>
> Set 1 .................................................
> - snip -
> Set 3950 .................................................
> Set 4000 100%
>
>
> PTRAJ: Successfully read in 4000 sets and processed 4000 sets.
>
> Dumping accumulated results (if any)
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri Apr 16 2010 - 14:30:02 PDT
