@ikegami thanks your reply. Now it gives an error:

 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scatte
+ring
 activities (A**4/AMU), depolarization ratios for plane and unpolarize
+d
 incident light, reduced masses (AMU), force constants (mDyne/A),
 and normal coordinates:
                     1                      2                      3
                     A                      A                      A
 atom        --    23.5214                40.9023                56.78
+56
 Red. masses --     6.7793                 1.0546                 5.56
+74
 Frc consts  --     0.0022                 0.0010                 0.01
+06
 IR Inten    --     2.4504                 0.2236                 0.61
+52
[download]

New version:

 
#!/usr/bin/env perl
use strict;
use warnings; 
use File::Path qw/make_path/;
use Cwd;

my $dir = cwd();

opendir (my $dh, $dir) or die "Unable to open current directory! $!\n"
+;
my @subdirs = grep { /^\.\.?\z/ } readdir($dh) or die "Unable to read 
+directory! $!\n";
closedir $dh;

my $result_path = "$dir/results";
make_path("$result_path");

for my $subdir ( sort @subdirs ) {

chdir($dir);

next unless -d $subdir;

make_path("$result_path/$subdir");

my $search_text1 = qr/atom/;
my $infile1="$subdir/input.txt";

   my $in_fh1;
   if (!open $in_fh1, '<', $infile1) {
      goto NEXT if $!{ENOENT};
      die qq{Failed to open "$infile1" for reading: $!};
   }

my $outfile1="$result_path/output";
    open $in_fh1, '<', $infile1  or die qq{Failed to open "$infile1" f
+or writing: $!};
    open my $out_fh1, '>', $outfile1 or die qq{Failed to open "$outfil
+e1" for writing: $!};
  while (<$in_fh1>) {
      next unless /$search_text1/;
      my @fields1 = split;
      print $out_fh1 join("\t", @fields1[1]), "\n";
      }
  close($in_fh1);
  close($out_fh1);

NEXT:
chdir("..");

}
[download]

Now it gives an error...

It still gives this "error" (not, in fact, an error but a warning) because the scalar expression  @fields1[1] (an array slice; see Slices in perldata) is still being used and is still better written as  $fields1[1] (please see above, first sentence).

---

Give a man a fish:  <%-(-(-(-<