Hello,
On Thu, Apr 8, 2010 at 12:35 AM, Jagdeesh C <jagc666.gmail.com> wrote:
> Dear Amber users,
>
> I am trying to do an analysis of my mdcrd file using ptraj. However trajin
> it is unable to open the mdcrd file. The same works when I have a smaller
> trajectory file.
> How do I solve my problem? The size of my present file is 6.2 Gb.
Try gzipping the file and reading in the gzipped mdcrd.
As a side note, consider using netcdf format (ioutfm=1 in sander/pmemd
input file). They are far faster to read, hold higher precision
numbers, and are far faster to write.
>
> Best regards,
> Jagdeesh.
>
>
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 10.0 integrated" (2/15/2008)
> -/- Executable is: "./ptraj"
> /-\
> \-/ Residue labels:
>
> MOL DG DG DG DT DT DA DG DG DG
> DT DT DA DG DG DG DT DT DA DG
> DG DG K+ K+ K+ K+ K+ K+ K+ K+
> K+ K+ K+ K+ K+ K+ K+ K+ K+ K+
> K+ WAT WAT WAT WAT WAT WAT WAT WAT WAT
> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
> ...
> WAT WAT WAT WAT WAT WAT WAT WAT
>
> Setting box to be an exact truncated octahedron, angle is 109.471221
>
> PTRAJ: Processing input from "STDIN" ...
>
> PTRAJ: trajin ./prodkn1.mdcrd 1 2000 1
> Checking coordinates: ./prodkn1.mdcrd
> trajin ./prodkn1.mdcrd ignored; could not open file (./prodkn1.mdcrd)
>
> PTRAJ: reference jag_kn_solvated.inpcrd
>
> Processing AMBER restart file jag_kn_solvated.inpcrd
>
> ....................................................................................................................
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Apr 07 2010 - 22:00:03 PDT
