The approach I gave would have worked if you had all of the list of filenames on the command line. If you want to take the list of filenames from a file, then we need to modify the input loop somewhat:

my @dssp_objs =();
#reads the files from the command line one line at a time.
while(<>)
{
    chomp; # remove the newline.
push @dssp_objs, Bio::Structure::SecStr::DSSP::Res->new('-file'=>$_);
}
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This code would read a line at a time out of DSSP_codes.txt (using your example).

I changed to the while(<>) loop just to be consistent with the way most people do this kind of loop. Since it automatically loads the $_ variable (and the loop is pretty short), I removed the $file variable. Otherwise, this is a drop-in replacement for the previous loop that should meet your needs.