Re: [AMBER] error ambpdb - Old style inpcrd file read

From: Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl>
Date: Wed, 20 Aug 2014 12:55:11 +0200

To my previous question: I attached a picture from vmd where I simply
loaded the prmtop and mdcrd file and this is what I got... the water is
very strange. What could be the problem?

Thank you in advance for your help.

/Urszula Uciechowska

> 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:
>
> | Flags: MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> and simulations stoped.
>
> the input file:
> production
> production
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 298.15, temp0 = 298.15,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 250000, dt = 0.002,
> ntpr = 200, ntwx = 200, ntwr = 200
> /
>
> Any ideas why this error comes up?
>
>
> Best regards
> Urszula Uciechowska
>
>
>
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/

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Received on Wed Aug 20 2014 - 04:00:02 PDT
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