What you need to do here is have your counter increment outside the scope of your main for loop. If I did this, I might code it like:

for my $file_no (1 .. 50) {
    my $filetag = "1AC$file_no";
    open my $fh, '>', "$filetag.mol" or die "Open fail for $filetag: $
+!";
    my @lines = generate_lines($file_no);
    for my $line (@lines) {
        print "$filetag $line\n";
    }
}
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If this is off point, try explaining how this algorithm (in pseudocode if necessary) missed. Reading Foreach Loops in perlsyn might be informative.