On Fri, Aug 19, 2011 at 5:19 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
> 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
>
But this is a compressed file. Try using cpptraj instead of ptraj for this
action (and make sure you have a fully patched version of AmberTools).
You could also try decompressing it (although you'll get good performance in
cpptraj even if you don't)
> 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.
>
What behavior are you seeing besides the checkCoordinates() warning above?
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 19 2011 - 16:00:03 PDT
