AMBER Archive (2006)

Subject: AMBER: Problems with carnal (Amber7)

From: anna.schrey_at_gmx.de
Date: Tue Oct 31 2006 - 09:24:29 CST

dear amber supporters,

I ran the following simulation

*******

cat << eof > dyn.in

# 200ps dynamics to heat and equilibrate the SH3 with NMR restraints
 &cntrl
   imin=0, nmropt=1,
   ntx=5, irest=1,
   ntrx=1, ntpr=5000,
   ntwr=5000,
   ntwx=5000,ntwv=5000,
   ntwe=5000,
   ntf=2,ntb=1,ntc=2,
   dielc=1,cut=8,
   scnb=2,scee=1.2,
   nsnb=25, nscm=500,
   ntr=0,nstlim=25100000,
   dt=0.002,temp0=280,
   ntt=1,
   tautp=1.0,ntc=2,
  &end
 &wt type='REST',istep1=1,istep2=100000,value1=1,value2=0, &end
 &wt type='REST',istep1=100001,istep2=25100000,value1=0,value2=0, &end
 &wt type='END' &end
LISTIN=sh3_cryst_NTV_50200ps_orest.restraints
LISTOUT=sh3_cryst_NTV_50200ps_orest.violations
DISANG=sh3_cryst_all.rst
eof
/usr/local/encap/mpich-126-intel-32/bin/mpirun -machinefile mpich_hosts1 -np 8 \
/swc/amber8/exe/pmemd -O -i dyn.in \
-o sh3_cryst_NTV_50200ps_orest.out -p sh3_cryst_water_ions.top \
-c sh3_cryst_NTV_eq.crd -ref sh3_cryst_NTV_eq.crd \
-r sh3_cryst_NTV_50200ps_orest.crd \
-x sh3_cryst_NTV_50200ps_orest.mdcrd -v sh3_cryst_NTV_50200ps_orest.mdvel \
-inf sh3_cryst_NTV_50200ps_orest.inf -e sh3_cryst_NTV_50200ps_orest.mden

*******

Trying to analyse the mdcrd file using carnal, I got the following out file:

*******

input average.inp
> # fit dynymics sh3_cryst_NTV_50200ps_orest on start structure SH3_13COM_NTV_eq2 makes average
> FILES_IN
> PARM p1 ../../sh3_cryst_water_ions.top;
Reading parm file (../../sh3_cryst_water_ions.top)
parm: opening ../../sh3_cryst_water_ions.top
> STREAM s1 WIN 40 4080 ../../sh3_cryst_NTV_50200ps_orest.mdcrd;
Using default parm (../../sh3_cryst_water_ions.top) for STREAM s1
 (box will be read from stream)
stream: opening ../../sh3_cryst_NTV_50200ps_orest.mdcrd
../../sh3_cryst_NTV_50200ps_orest.mdcrd: sys err Value too large for defined data type

********

can you tell me what is wrong? Is the file too big for carnal analysis?

best regards,

Anna Schrey 

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