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
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Received on Wed Jan 23 2013 - 05:00:02 PST
