On Tue, 2014-08-19 at 13:01 +0200, Urszula Uciechowska wrote:
> Dear amber users,
>
> I am trying to run ambpdb -p *.prmtop <*.crd> *.pdb and I am getting:
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/09/14 Time = 15:01:14
> forrtl: severe (64): input conversion error, unit 5, file stdin
> Image PC Routine Line Source
> ambpdb 00000000004AB78A Unknown Unknown Unknown
> ambpdb 00000000004AA286 Unknown Unknown Unknown
> ambpdb 00000000004633E0 Unknown Unknown Unknown
> ambpdb 000000000042C30E Unknown Unknown Unknown
> ambpdb 000000000042B84F Unknown Unknown Unknown
> ambpdb 0000000000448392 Unknown Unknown Unknown
> ambpdb 0000000000413F21 Unknown Unknown Unknown
> ambpdb 00000000004069A3 Unknown Unknown Unknown
> ambpdb 00000000004031CC Unknown Unknown Unknown
> libc.so.6 00007FCDA3AFE1A6 Unknown Unknown Unknown
> ambpdb 00000000004030C9 Unknown Unknown Unknown
>
> What did go wrong? Calculations are still running and seem to be ok.
If I had to guess (and that's all I can do based on the information),
the coordinate file you're redirecting to ambpdb is not an inpcrd or
restart file. My guess is that it's a trajectory file. Or maybe it's a
NetCDF restart file.
In either case, ambpdb requires an ASCII restart file. If you have a
different type of coordinate file, you need to use cpptraj instead.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 19 2014 - 04:30:04 PDT
