Shell Programming and Scripting

#!/bin/bash

count=1
while read line
do
    if (($count > 4)); then
        awk -v var1="$count" '{printf "%3s%8s%11s%11s%11s\n",var1,$2,$3,$4,$5}'
    else
        echo $line
    fi
count=$((count+1))
done < posre_sub.itp > test

cat test

$ cat origamisven.sh
#!/bin/bash

count=1
while read line
do
    if (($count > 3)); then
        num_line=$((++num_line))
        echo "$line" | awk -v var1="$num_line" '{printf "%3s%8s%11s%11s%11s\n",var1,$2,$3,$4,$5}'
    else
        echo $line
    fi
count=$((count+1))
done < posre_sub.itp > test

cat test
$ bash origamisven.sh 
; position restraints for System_&_XYL of Protein in water
[ position_restraints ]
; i funct fcx fcy fcz
  1       1        100        100        100
  2       1        100        100        100
  3       1        100        100        100

# NR is the line number.  So, for lines 4 and up, set the first record,
# aka $1, to the line number minus three.
# The 1 after the } makes it print every line.
$ awk '{ if(NR>3) $1=NR-3 } 1' < data
; position restraints for System_&_XYL of Protein in water
[ position_restraints ]
; i funct fcx fcy fcz
1 1 100 100 100
2 1 100 100 100
3 1 100 100 100
$