Well, you WRITE that your input file asks for trajin md20.mdcrd
but the ptraj output says otherwise:
> PTRAJ: trajin m19.mdcrd
> Checking coordinates: m19.mdcrd
> Could not process trajectory m19.mdcrd
So, the answer is that your input is NOT what you claim it is.
I would make sure that the md*.mdcrd files are for sure in that same
directory. ptraj is unable to find at least the 19 one.
Adrian
On 6/14/11 9:12 AM, fatahiya wrote:
> i'm trying to do secondary structure analysis
> my input file is:
>
> trajin md20.mdcrd
> secstruct out md20.ss time 0.2 :1-20
>
> the output is:
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 11.0 integrated" (4/2010)
> -/- Executable is: "ptraj"
> /-\ Running on 1 processor(s)
> \-/ Residue labels:
>
> ASN LEU TYR ILE GLN TRP LEU LYS ASP GLY
> GLY PRO SER SER GLY ARG PRO PRO PRO SER
> Cl- 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 m19.mdcrd
> Checking coordinates: m19.mdcrd
> Could not process trajectory m19.mdcrd
>
> PTRAJ: secstruct out md19.ss :1-20 time 0.2
> Mask [:1-20] represents 304 atoms
> WARNING in ptraj(): No input trajectories specified (trajin), aborting...
>
> can anybody help me how to do secstruct analysis?
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Tue Jun 14 2011 - 00:30:05 PDT
