Dear specialists,
I ran a simulation with a setup as follows:
cat << eof > dyn.in
# 400ps dynamics to drop the restraints
&cntrl
imin=0, nmropt=1,
ntx=5, irest=1,
ntrx=1, ntpr=1000,
ntwr=1000,
ntwx=1000,ntwv=1000,
ntwe=1000,
ntf=2,ntb=1,
dielc=1,cut=8,
scnb=2,scee=1.2,
ntr=0,nstlim=200000,
dt=0.002,temp0=280,
ntt=1,
tautp=1.0,ntc=2,
&end
&wt type='END' &end
LISTIN=SH3_13COM_HB_NTV_eq2.restraints
LISTOUT=SH3_13COM_HB_NTV_eq2.violations
DISANG=SH3_cryst_COM_HB_end.rst
eof
/usr/local/encap/mpich-126-intel-32/bin/mpirun -machinefile mpich_hosts -np 8 \
/swc/amber8/exe/pmemd -O -i dyn.in -o SH3_13COM_HB_NTV_eq2.out \
-p SH3_13COM.top -c SH3_13COM_HB_NTV_eq.crd -ref SH3_13COM_HB_NTV_eq.crd \
-r SH3_13COM_HB_NTV_eq2.crd -x SH3_13COM_HB_NTV_eq2.mdcrd -v SH3_13COM_HB_NTV_eq2.mdvel \
-inf SH3_13COM_HB_NTV_eq2.inf -e SH3_13COM_HB_NTV_eq2.mden
Trying to use the restart file for a follow-up simulation, it failed. Trying to create a PDB file from the restart file gave the following error message:
| New format PARM file being parsed.
| Version = 1.000 Date = 03/24/06 Time = 13:17:12
fmt: read unexpected character
apparent state: unit 5 (unnamed)
last format: (6F12.7)
lately reading sequential formatted external IO
Abort
The .mdcrd file can be read properly by software such as vmd, whereas a CARNAL dump of the last frame resulted in a distorted structure.
Sometimes, this problem could be avoided by wrappig the trajectory, but not this time.
Thanx for answers,
Anna
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Received on Sun Jun 18 2006 - 06:07:25 PDT
