Hi,
There was an issue in AT1.4 ptraj when determining the number of
frames in large (> 2GB) GZ-compressed Amber trajectories that was
addressed by bugfix 16. Make sure you've applied all the AT 1.4
bugfixes (
http://ambermd.org/bugfixesat.html).
However, as Jason said, upgrading to AmberTools12 is probably your
best bet (
http://ambermd.org/AmberTools-get.html).
-Dan
On Wed, Jan 23, 2013 at 5:52 AM, Kamali Sripathi <ksripath.umich.edu> wrote:
> Dear AMBER users,
>
> I've found a problem when analyzing AMBER10 trajectories using
> AmberTools1.4 on my personal computer. I get this error:
>
> *PTRAJ: trajin production1.traj.gz*
> * Checking coordinates: production1.traj.gz*
> *checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: production1.traj.gz*
> * If this is not a compressed file then there is a problem*
> *Rank: 0 Atoms: 58226 FrameSize: 1414917 TitleSize: 81 NumBox: 3 Seekable 0*
>
> which I know typically indicates that the topology and trajectory files fed
> into ptraj are different. I know that can't be the problem in my case,
> however, since I use the same topology file that I used to write the
> trajectory in the first place, and I've successfully used this pair with
> ptraj on a different cluster. I have to assume, then, that the problem is
> because my production files are written using AMBER10, and the AmberTools
> on my computer is version 1.4. Interestingly, I do not see this error when
> analyzing joined, stripped trajectories from the same simulation.
>
> I was wondering if there was patch or modification I could apply that would
> let me analyze raw trajectories on my computer using the newer version of
> AmberTools? I've looked a bit in the mailing list archives and in the
> AmberTools manual, but haven't found an answer to my question so far.
> Please do let me know if I've missed something, however.
>
> Thank you all, and have a great day,
> --
> Kamali Sripathi
> PhD Candidate, Medicinal Chemistry
> Walter Laboratory
> 930 North University
> Ann Arbor, MI, 48109
> ksripath.umich.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
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 Wed Jan 23 2013 - 08:00:02 PST
