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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Received on Wed Aug 20 2014 - 05:00:02 PDT
