Thanks Jason and Dan. Quick question: aside from pathname confusion, is
there any reason why I shouldn't have AT1.4 and AT12 on my computer at the
same time? I'm not really sure of the most effective way to uninstall
AT1.4, and I wouldn't want to waste time figuring it out.
Dan, you were right: my raw production files are ~ 2.6 GB, so the bugfix
might just fix everything.
Thanks so much again,
Kamali
On Wed, Jan 23, 2013 at 10:31 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 23 2013 - 15:00:03 PST
