bash: sed processing of the files including leading-zeros - bash

Question

I am using a bash script to loop over the files pre-defined in several groups of the array within the directory in order to edit the file in case if its exist (for example in the 1st group there are 100 files arranged from 0001 to 0100, in the second group - 50 files arranged from 0001 to 0050 etc).
#an array for the groups
systems=(one two three four)
# loop over the groups
for file in "${systems[#]}"; do
i="1"
# introduce K var because the files are numbered as 0001 ... 0100
k=$(printf '%03d' $i)
while [ $i -le 100 ]; do
if [ ! -f "${output}/${file}_${k}.pdb" ]; then
echo 'File '${output}/${file}_${k}.pdb' does not exits!'
break
else
## edit file via SED
# to add i-th number on the first string of the file and substitute smth on the last string;
sed -i -e '1 i\MODEL '$i'' -e 's/TER/ENDMDL/g' ${output}/${file}_${k}.pdb
((i++))
fi
done
done
This script doesn't not work on the stage of SED editing, but if I omit usage of the leading zeros in the names of files and use just i-th index within the script, everything works fine:
# loop over the groups
for file in "${systems[#]}"; do
i="1"
# put k into comment since filles arranged from 1 to 100 without leading zeros;
#k=$(printf '%03d' $i)
while [ $i -le 100 ]; do
# the filles arranged from 1 to 100
if [ ! -f "${output}/${file}_${i}.pdb" ]; then
echo 'File '${output}/${file}_${i}.pdb' does not exits!'
break
else
## edit file via SED
# to add i-th number on the first string of the file
sed -i -e '1 i\MODEL '$i'' -e 's/TER/ENDMDL/g' ${output}/${file}_${i}.pdb
((i++))
fi
done
done

Answer 1

k is assigned before the loop with i
i="1"
# introduce K var because the files are numbered as 0001 ... 0100
k=$(printf '%03d' $i)
while [ $i -le 100 ]; do
...
((i++))
...
done
Move the assignment to k inside the loop.
Alternative:
for ((i=1;i<100;i++)); do
k=$(printf '%03d' ${i})
...

Answer 2

NOTE: have made several edits.
No answers of my own here - just compiling into a single block of code, incorporating the the answers of jas (at his request) and Walter A who likely hit the real problem -
for file in "${systems[#]}"
do for ((i=1;i<100;i++))
do printf -v enumerated "${output}/${file}_%04d.pdb" $i
if [[ -f "$enumerated" ]
then sed -i -e "1 i\\MODEL $i" -e 's/TER/ENDMDL/g' $enumerated
else echo "file not found: '$enumerated''
fi
done
done
Depending on what else is in your directory structure, you might also try this:
for stub in "${systems[#]}"
do for file in "$output/${stub}"_[0-9][0-9][0-9][0-9].pdb
do sed -i -e "1 i\\MODEL ${file//[^0-9]/}" -e 's/TER/ENDMDL/g' "$file"
done
done