Shell Programming and Scripting

Hello Guys,
I have written the following script to do certain job. I have more than 300 files, all are .pdb & .out files. and the files are (1,3,5,7,11,13,15,17,21,.......787,791,793,795).pdb /.out . But the way I created the for loop in my script works only one file at a time. But that is not the purpose of a for loop. So could you please help me how can I modify for loop in the following script so the script can process all the files a single run. thanks advance!


for ((i=131;i<=131;i++)); do

awk '{gsub("PW " ,"TRP"); print}' $i.pdb > $i.amberized.pdb

awk -f ./get.amber.parm.10.awk ./$i.modified.pdb 1.07 1.0 > ./$i.amberized.pdb


tstart=`grep -an -w "Atom No." $i.out | awk '{print $1}' | sed "s/:/ /" | awk '{print $1+1}'`


tstop=`echo $tstart | awk '{print $1+2962}'`


head -$tstop $i.out | tail -2963 > tmp

cut -c 1-55 $i.amberized.pdb > first_half
cut -c 65- $i.amberized.pdb > end
cut -c 27-35 tmp > charges
paste -d '' first_half charges | paste -d '' - end > $i.AM1.pdb

# exit

rm tmp >& /dev/null;
rm end >& /dev/null;

rm charges >& /dev/null;
rm first_half >& /dev/null;
done

You can do something like that (with bash, the extglob option must be set) :

Code:

ls -1 +([0-9]).pdb |
while read pdb_file
do
   i=${pdb_file%.pdb}

   . . . . 

done

or

Code:

for pdb_file in $(ls -1 +([0-9]).pdb
do
   i=${pdb_file%.pdb}

   . . . . 

done

thanks..it works smoothly