What do you mean by "doesn't work"? Is the number of F's too big? Does the program output any error messages?

When glaring at your script, I can see that

• you do not chomp the $proteinfilename after reading it from STDIN. The real file name probably does not contain a newline at the end.
• if the open is not successful, your program continues. Are you really interested in the results, if the file cannot be found? Use the idiom

  open my $FH, '<', $filename or die "Cannot open: $!";
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• next takes a label as a parameter. There are no labels in your code.
• you do not indent the code. Once you are advanced enough to use loops, please also learn to indent the code. Without indentation, your code becomes write-only, unreadable mess for humans.