I may have not understood your script, but this is the general idea:

#!/usr/bin/perl -w
use strict; 

# usage: AskAtom.pl SomeFile
#   First line of "SomeFile" is the output file name.
#   Program asks the user for a value which is
#   appended to each line of the subsequent lines
#   in "SomeFile".

my ($fileIN) = @ARGV; #first command line arg is $fileIN

open(my $in, "<", $fileIN) or die "Can't open $fileIN: $!";

#The $newFile name is on the first line of "somefile"

my $newFile = <$in>;  #read the first line of $fileIN
$newFile =~ s/^\s*//; #delete leading spaces (optional)
$newFile =~ s/\s*$//; #delete trailing spaces (also does chomp())

my $atom = ask_user4atom();

open (my $out, ">", $newFile) or die "Can't write to $newFile :$!";

while (<$in>) #reading of <$in> starts again at 2nd line
{
   chomp;             #deletes line endings
   next if /^\s*$/;   #skip blank lines (a blank line at the end 
                      # of the file is not an error) 
   print $out "$_-$atom\n"; #append $atom to each line
}

#When asking user a question - blank line is just a
#re-prompt. Spaces before or after the user input
#also do not matter...That is standard CMD Line...

sub ask_user4atom
{
    my $atom;
    while ( (print "Enter atom symbol: "), $atom =<STDIN>)
    {
       next if $atom =~ /^\s*$/; #re-prompt on a blank line
       $atom =~ s/^\s*//;        #delete leading spaces
       $atom =~ s/\s*$//;        #delete trailing spaces
       return $atom;
    }
}

#Note: In a short running script like this, there is
# no need to explictly close() files. The O/S will do that
# when the script finishes - no biggie.
# A File Handle is an O/S resource, but here this is not
# significant.


=Example file: ChemIn.txt
Chemout.txt
ABC
XYZ
=End ChemIn.txt

=Example Command Line Output

C:\TEMP>perl askatom.pl ChemIn.txt
Enter atom symbol:
Enter atom symbol:    Na

C:\TEMP>type ChemIn.txt
ChemOut.txt
ABC
XYZ

C:\TEMP>type ChemOut.txt
ABC-Na
XYZ-Na

=END of Example Command Line Output
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