Jason,
Many thanks. The decompressed file works with ptraj.
All the best
George
On Aug 20, 2011, at 12:51 AM, Jason Swails wrote:
> 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 Sat Aug 20 2011 - 04:30:04 PDT
