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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 28 2011 - 20:30:02 PDT
