My mistake, I am using *.rst file
ambpdb -p *.prmtop <*.rst> *.pdb
Urszula Uciechowska
> 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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>
>
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Received on Tue Aug 19 2014 - 04:30:05 PDT
