Further to my earlier message and having checked the archive for similar error messages, I came across Prof. Case's message (
http://archive.ambermd.org/201006/0515.html). As my reference pdb file was from the Protein Data Bank, I stripped the headers, as suggested.
The error message that is now issued is the following:
checkCoordinates(): Could not predict number of frames for AMBER trajectory file: prod_2ns.mdcrd.gz
If this is not a compressed file then there is a problem
I've conducted a number of different analyses with this trajectory file and the corresponding prmtop file without any hitches.
So, I'm rather baffled by this behaviour.
Regards
George
On Aug 19, 2011, at 8:12 PM, George Tzotzos wrote:
> Hi everybody,
>
> I'm following the procedure described in TUTORIAL B3 - SECTION 6
>
> I'm getting the following error message on applying ptraj to the following script (rmsd_ref.in)
>
> trajin prod_2ns.mdcrd.gz
> reference xl_structure.pdb
> rms reference out rmsd_to_xl_structure.dat .N,CA,C time 1.0
>
>
> $ ptraj 1dqe_bom_solv.prmtop <rmsd_ref.in > measure_rmsd.out
>
> checkCoordinates(): Could not predict number of frames for AMBER trajectory file: prod_2ns.mdcrd.gz
> If this is not a compressed file then there is a problem
> readAmberRestart(): sscanf on atoms and time in restart file xl_structure.pdb failed
>
>
> In the procedure described in the tutorial there's no restart file. Or am I wrong?
>
> Any help would be much appreciated
>
> Regards
>
> George
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Received on Fri Aug 19 2011 - 14:30:02 PDT
