AMBER Archive (2006)

Subject: AMBER: Problems with carnal (Amber7)

Date: Tue Oct 31 2006 - 09:24:29 CST

dear amber supporters,

I ran the following simulation


cat << eof >

# 200ps dynamics to heat and equilibrate the SH3 with NMR restraints
   imin=0, nmropt=1,
   ntx=5, irest=1,
   ntrx=1, ntpr=5000,
   nsnb=25, nscm=500,
 &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
/usr/local/encap/mpich-126-intel-32/bin/mpirun -machinefile mpich_hosts1 -np 8 \
/swc/amber8/exe/pmemd -O -i \
-o sh3_cryst_NTV_50200ps_orest.out -p \
-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
> PARM p1 ../../;
Reading parm file (../../
parm: opening ../../
> STREAM s1 WIN 40 4080 ../../sh3_cryst_NTV_50200ps_orest.mdcrd;
Using default parm (../../ 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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