Have you applied all bugfixes for AmberTools 1.4? Specifically, bugfix 16 is
supposed to fix this problem for AmberTools 1.4.
I hope that helps.
-Bill
On Thu, Apr 28, 2011 at 11:14 PM, Nicole A. Horenstein
<horen.chem.ufl.edu>wrote:
> Hi all, is there an upper limit to size that ptraj can handle on reading in
> a formatted trajectory? I found the following trouble with AmberTools 1.4
> or 1.5 (patched).
>
> Large files eg 3-5 GB give an error message in ptraj:
>
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: S36CYZMDproduction2.mdcrd
> If this is not a compressed file then there is a problem
> Rank: 0 Atoms: 125003 FrameSize: 3037598 TitleSize: 81 NumBox: 3 Seekable 0
>
>
> These large files were not in compressed format. When smaller (from prior
> runs in the series) files were tried, ptraj works fine. When I restarted the
> trajectory and output in NETCDF format, I was able to read in to ptraj
> (though thus far, the file is quite small). Any sense of what is up- I do
> not know how to interpret this result with large files.
> Thank you-
> Nicole
>
> Dr. Nicole Horenstein
> Associate Professor of Chemistry
> Department of Chemistry
> University of Florida
> Gainesville FL, 32611
> U.S.A.
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Thu Apr 28 2011 - 20:30:03 PDT
