open(IN, "/path/outModified.pl") or die "$!";

while (my $line = <IN>) {
chomp($line);
my @array = (split (/\s+/, $line))[6, 7, 8];
# print "@array\n";
push @points, [ @array ];
}

close(IN);

print '@points : ', Dumper \@points;

open my $out_file, '>', "/path/dist_modified.pl" or die "cannot open: $!\n";

for my $i1 ( 0 .. $#points -1 ){
my ( $x1, $y1, $z1 ) = @{ $points[$i1] };
for my $i2 ( 1 .. $#points){
my ( $x2, $y2, $z2 ) = @{ $points[$i2] };
my $dist = sqrt(($x2 - $x1)**2 + ($y2 - $y1)**2 + ($z2 - $z1)**2);
print $out_file "153L.pdb: the distance between CA $i1 and CA $i2 = $dist\n";
}
}
close $out_file or die "cannot close file: $!\n";