shell: strange string concatenation behavior [duplicate]

Answer 1

The "string goes to the beginning of the line" is symptomatic of a carriage return in your $line that you can among many other ways remove with a tr pipe to your file:

while IFS= read -r line
do
  echo "line ${line}"
  pdbfile=${line}.pdb  
  echo "pdbfile ${pdbfile}"
done < <(tr -d '\r' <file)

Answer 2

I've tried your script and it works fine for me:

./testConcat
line pdb8mhtA
pdbfile pdb8mhtA.pdb

btw you could try to "preserve" the "."

while read line
do
  echo line ${line}
  pdbfile=${line}\.pdb
  echo pdbfile ${pdbfile}
done < myfile

as you can see the result is the same

./testConcat
line pdb8mhtA
pdbfile pdb8mhtA.pdb