[AMBER] ambpdb problem with binary restart file

From: Date, Mihir <Mihir.Date.STJUDE.ORG>
Date: Wed, 13 Nov 2013 12:43:02 -0600

I have production run of my system which was generated using netcdf binary format for trajectory as well as binary format for restart files (using ntxo = 2).
I am trying to get a pdb file from restart file using following command

$ ambpdb -bin -p complex-tip3.prmtop < prod-NVT-20ns.rst > prod-NVT-20ns.pdb

and I get following error message.

| New format PARM file being parsed.
| Version = 1.000 Date = 11/08/13 Time = 12:25:34
At line 889 of file ambpdb.F90 (unit = 5, file = 'stdin')
Fortran runtime error: Missing format for FORMATTED data transfer

I checked line 889 of ambpdb.F90 and it seems there is something wrong/unreadable with the title of my binary restart file. (?? you can also correct me if this is not right)
Can someone give me possible solution on it.
I have long runs of MD (more than 50ns). I am using the binary format for trajectory as well as restart file so as to avoid character limit problem in these files and avoid post-processing for re-centring.

Thanks in advance


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Received on Wed Nov 13 2013 - 11:00:02 PST
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