> How did you check the rst file? Did you just open it up in a text
> editor and inspect it?
Yes I simply open it in a text editor. I also run ptraj and it wokred for
the mdcrd file. What can I do more? How to carry on the simulations?
I have also tried to rerun this part couple of times but ended up with the
same error.
/Urszula
> On Wed, 2014-08-20 at 10:20 +0200, Urszula Uciechowska wrote:
>> Dear AMBEr users,
>>
>> I am not able to convert my *.rst file into the *pdb - the command I
>> used
>> is ambpdb -p prmtop <*rst> *.pdb. It is very strange as the simulations
>> are run for 30ns.
>> after running ambpdb -I have
>>
>> | 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
>> libintlc.so.5 00007FF4C016B9AA Unknown Unknown
>> Unknown
>> libintlc.so.5 00007FF4C016A4A6 Unknown Unknown
>> Unknown
>> libifcore.so.5 00007FF4C11297AC Unknown Unknown
>> Unknown
>> libifcore.so.5 00007FF4C109CE42 Unknown Unknown
>> Unknown
>> libifcore.so.5 00007FF4C109C2E6 Unknown Unknown
>> Unknown
>> libifcore.so.5 00007FF4C10D7C34 Unknown Unknown
>> Unknown
>> ambpdb 0000000000410E0D Unknown Unknown
>> Unknown
>> ambpdb 0000000000404325 Unknown Unknown
>> Unknown
>> ambpdb 000000000040120C Unknown Unknown
>> Unknown
>> libc.so.6 00007FF4BFC0F1A6 Unknown Unknown
>> Unknown
>> ambpdb 0000000000401109 Unknown Unknown
>> Unknown
>>
>> I have chcecked the *rst file and seems to be ok and the simulations
>> finished correctly. However when I try to use this *rst file for the
>> next
>> production run I got an error in *out file:
>
> How did you check the rst file? Did you just open it up in a text
> editor and inspect it?
>
> Try loading it into cpptraj. If cpptraj does not read your rst file
> (which I suspect it won't), then you will basically have irrefutable
> confirmation that your file is somehow broken. Maybe it's truncated.
> Maybe there are *** characters filling out one of the fields. I don't
> know without being able to see the file.
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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http://www.ug.edu.pl/
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Received on Wed Aug 20 2014 - 05:00:03 PDT
