Hi,
Have you tried running ptraj on just this file? Can you open it in a
text editor like vi? Is there any reason to suspect that it is
corrupted (e.g. the file size is shorter than expected or something)?
You could try running ptraj with more verbose messages to see if you
can get some more info on why the file cannot be opened:
prnlev 5
trajin md10.mdcrd
go
Also, what version of AmberTools are you running and what bugfixes
have been applied?
-Dan
On Tue, Jul 19, 2011 at 9:11 AM, David Condon <dec986.gmail.com> wrote:
> Hello Amber Experts,
>
> I am running the following script to combine trajectory files, with
> $ptraj prmtop < combine:
>
> trajin md3.mdcrd
> trajin md4.mdcrd
> trajin ...
> trajin md12.mdcrd
> trajout mdall.mdcrd
>
> For reasons beyond me, there is something wrong with md10.mdcrd:
>
> PTRAJ: trajin md9.mdcrd
> Checking coordinates: md9.mdcrd
>
> PTRAJ: trajin md10.mdrcd
> Checking coordinates: md10.mdrcd
> Could not open file (md10.mdrcd) with mode (r)
> trajin md10.mdrcd ignored; could not open file (md10.mdrcd)
>
> PTRAJ: trajin md11.mdcrd
> Checking coordinates: md11.mdcrd
>
> Similar error messages are in the AMBER archives, but I did specify
> the prmtop file (http://archive.ambermd.org/200503/0312.html) and the
> permissions on all of the files are identical. This is a 64 bit
> machine and the file is ~110 MB
> (http://structbio.vanderbilt.edu/archives/amber-archive/2005/3108.php).
>
> Can this be fixed or do I have to re-run the simulation?
>
> Thanks for your time!
> -Dave
>
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>
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Received on Tue Jul 19 2011 - 08:30:02 PDT
