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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Received on Wed Nov 01 2006 - 06:07:30 PST
