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!
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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Received on Fri May 06 2011 - 08:00:04 PDT
