Try upgrading to AmberTools 12, possibly using cpptraj instead of ptraj
(it's used the same way).
Also, a good way of determining whether or not the prmtop and trajectories
are really compatible is to visualize the system using VMD or another MD
visualization program. (You will probably have to decompress the file
first).
HTH,
Jason
On Wed, Jan 23, 2013 at 7:52 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 23 2013 - 05:30:02 PST
