On Fri, May 6, 2011 at 4:54 PM, Katharina Lang <katharina.lang.kit.edu>wrote:
> Hello,
>
> I found out that the dyn.crd (which seems to be unit -5) was too large for
> Amber to handle it. Since the coordinate file was from a heat-up
> simulation,
> I actually only needed the heated up molecule. So, I changed the "-c
> dyn.crd" to "-c dyn.rst" and everything worked out!
>
Oh! The -c should *not* take a trajectory file. The problem is not that
the inpcrd file is too large, the problem is that the format that the inpcrd
file expects is different than the format of the trajectory file, so it
*has* to fail with this error.
All the best,
Jason
> Greetings,
> Katharina
>
> -----Ursprüngliche Nachricht-----
> Von: Katharina Lang [mailto:katharina.lang.kit.edu]
> Gesendet: Friday, April 29, 2011 16:33
> An: amber.ambermd.org
> Betreff: [AMBER] forrtl: severe (64): input conversion error, unit -5,file
> Internal Formatted Read
>
> Dear Amber community,
>
>
>
> I have this error message when simulating Lysozyme with pH control:
>
> forrtl: severe (64): input conversion error, unit -5, file Internal
> Formatted Read
>
> Image PC Routine Line Source
>
>
> libintlc.so.5 00007FCCEF27351D Unknown Unknown Unknown
>
> libintlc.so.5 00007FCCEF272025 Unknown Unknown Unknown
>
> libifcoremt.so.5 00007FCCEF4900BC Unknown Unknown Unknown
>
> libifcoremt.so.5 00007FCCEF3FDC1F Unknown Unknown Unknown
>
> libifcoremt.so.5 00007FCCEF3FD381 Unknown Unknown Unknown
>
> libifcoremt.so.5 00007FCCEF42FCC5 Unknown Unknown Unknown
>
> libifcoremt.so.5 00007FCCEF42D80D Unknown Unknown Unknown
>
> sander.MPI 00000000005305AA Unknown Unknown Unknown
>
> sander.MPI 00000000004E571C Unknown Unknown Unknown
>
> sander.MPI 00000000004E3EFB Unknown Unknown Unknown
>
> sander.MPI 000000000044A87C Unknown Unknown Unknown
>
> libc.so.6 00007FCCEED09BC6 Unknown Unknown Unknown
>
> sander.MPI 000000000044A779 Unknown Unknown Unknown
>
>
>
> Before starting this simulation, I ran a short energy minimization and then
> heat up the system to 300K. Both simulations were successful. I checked the
> rst-file and there are no ****s in it.
>
>
>
> I submit the pH control job with “/opt/openmpi/1.5/bin/mpirun
> $AMBERHOME/exe/sander.MPI -O -i dyn_pH2.in -o dyn_pH2.out -c dyn.crd -p
> prm.top -r dyn_pH2.rst -x dyn_pH2.crd -cpin cp.in -cpout cp.out -cprestrt
> cp.rst” and the dyn_pH2.in file is:
>
>
>
> &cntrl
>
> icnstph = 1,
>
> solvph = 2,
>
> ntcnstph = 5,
>
> dt = 0.002,
>
> cut = 30.0,
>
> igb = 2,
>
> saltcon = 0.1,
>
> ntb = 0,
>
> nrespa = 1,
>
> ntt = 1,
>
> tempi = 300.0,
>
> temp0 = 300.0,
>
> tautp = 2.0,
>
> ntc = 2,
>
> ntf = 2,
>
> tol = 0.000001,
>
> /
>
>
>
> I get the same error for different pH values. Do you have any ideas, where
> I
> am going wrong?
>
>
>
> Best regards,
>
> Katharina Lang
>
>
>
> Karlsruhe Institute of Technology (KIT)
> Institute of Engineering in Life Sciences
>
> <http://mab.ciw.uni-karlsruhe.de/english/index.php> Section IV:
> Biomolecular Separation Engineering
>
> Dipl.-Ing. Katharina Lang
>
> <http://dict.leo.org/ende?lp=ende&p=5tY9AA&search=Ph> Ph.
> <http://dict.leo.org/ende?lp=ende&p=5tY9AA&search=D> D.
> <http://dict.leo.org/ende?lp=ende&p=5tY9AA&search=student> student
>
> Email: <mailto:vorname.nachname.kit.edu> katharina.lang.kit.edu
> <http://www.kit.edu/> www.kit.edu
>
> KIT – University of the State of
>
> Baden-Württemberg and National
>
> Laboratory of the Helmholtz Association
>
>
>
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri May 06 2011 - 09:30:12 PDT
