Hi guys, I am running a shell script but problem appeared. I don't know
what's wrong. My shell script reads like:
#!/bin/sh
###take snapshots at 100ps generate reference files
cat<<EOF>ptraj.in
trajin wt1mg_dry.crd 1 100 10
trajout wt1mg_ref restart
go
EOF
ptraj wt1mg_dry.parm7 ptraj.in
###calculate the rmsd for each reference structure
for ref in wt1mg_ref*;do
set ofile=$ref.rms
cat<<EOF>rms.ptraj
trajin wt1mg_dry.crd 1 100
reference $ref
rms reference out $ofile.rms :1-154
go
EOF
ptraj wt1mg_dry.parm7 rms.ptraj
done
###clean up the files and merge them into a single file
cp wt1mg_ref.2.rms rms1
set i=10
while ( $i <=100 );do
cut -b12-20 wt1mg_ref.$i.rms>tmp
paste rms1 tmp>rms
cp rms rms1
. i=$i+10
done
rm *.rms rms1 tmp
mv rms relax.rms
It is anticipated to get a file named "relax.rms ", but no file was created
when I tried the third part of my script. The error showed that no
"wt1mg_ref.2.rms" was found.
Thanks in advance.
Yours,
Tianyuan
--
Bioengineering
School of Life Science and Technology
Xi'an Jiaotong University
oceanrabbit.mty.gmail.com
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Received on Mon May 24 2010 - 03:00:07 PDT
