Hi,
On Fri, Jun 25, 2010 at 7:55 PM, Paul S. Nerenberg <psn.berkeley.edu> wrote:
>
> I recompiled AmberTools 1.4 today after applying the latest bugfixes
> and this seems to have somehow broken ptraj's ability to analyze
> gzipped trajectory files. When running "make test", this build passed
> everything fine (zero reported errors), but I'm not sure what, if any,
> compressed trajectories are encountered by ptraj during those tests.
The ptraj_trajectory test checks ptraj's ability to read in compressed
and uncompressed trajectories.
What is very strange to me is the inconsistent behavior of ptraj with
respect to your uncompressed trajectories:
[UNCOMPRESSED AFTER BUGFIX]
>
> PTRAJ: trajin ./mdcrd/ala3_wat_prod2_s1.mdcrd
> Checking coordinates: ./mdcrd/ala3_wat_prod2_s1.mdcrd
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: ./mdcrd/ala3_wat_prod2_s1.mdcrd
> If this is not a compressed file then there is a problem
> Rank: 0 Atoms: 2396 FrameSize: 58248 TitleSize: 81 NumBox: 3 Seekable 0
[UNCOMPRESSED BEFORE BUGFIX]
>
> PTRAJ: trajin ./mdcrd/ala3_wat_prod2_s1.mdcrd
> Checking coordinates: ./mdcrd/ala3_wat_prod2_s1.mdcrd
> Rank: 0 Atoms: 2396 FrameSize: 58248 TitleSize: 81 NumBox: 3 Seekable 1
Ptraj determines the number of frames in an Amber Trajectory by using
the total file size and the expected frame size in bytes based on the
total number of atoms. I've run some tests of my own using AT1.4 ptraj
(w/latest bugfixes) and I can't reproduce the behavior you are seeing,
which suggests it may be a Mac-specific bug.
[My test: COMPRESSED AFTER BUGFIX]
PTRAJ: trajin run0.crd.gz
Checking coordinates: run0.crd.gz
Rank: 0 Atoms: 49115 FrameSize: 1193520 TitleSize: 30 NumBox: 3 Seekable 1
[...]
INPUT COORDINATE FILES
File (run0.crd.gz) is an AMBER trajectory (with box info) with 100 sets
[My test: UNCOMPRESSED AFTER BUGFIX]
PTRAJ: trajin run0.crd
Checking coordinates: run0.crd
Rank: 0 Atoms: 49115 FrameSize: 1193520 TitleSize: 30 NumBox: 3 Seekable 1
[...]
INPUT COORDINATE FILES
File (run0.crd) is an AMBER trajectory (with box info) with 100 sets
If possible, could you rerun all 4 tests you did (pre-bugfix with and
without compression, and post-bugfix with and without compression) but
insert this line at the top of your ptraj input:
prnlev 5
Then redirect the stdout and stderr to a file and send them my way? For example:
ptraj.in:
prnlev 5
trajin ./mdcrd/ala3_wat_prod2
....
go
ptraj prmtop ptraj.in > ptraj.out 2>&1
Thanks!
-Dan
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Wed Jun 30 2010 - 07:00:04 PDT
