Ok in short my input and output both are divided in blocks. My 1st problem 1) In the output of *vertices portion my code prints

But in actual I want it to print the first two columns of the only first energy block like

My code for this section is

$data_file="HIVgag.ct";

open(MYFILE, $data_file) || die("Could not open file!");
$b=$between=$energy=0;
while (<MYFILE>) {
    if (/energy/i) {
        $energy++;
        $between=$b;
    }
    elsif ($energy) {$b++}
}


close(MYFILE);

open(MYFILE, $data_file) || die("Could not open file!");
open(WRITE, ">final.net");
print WRITE "*vertices $between\n";

 while(<MYFILE>)
 {
 foreach $row (<MYFILE>)
 {
 @row = $row;
(@row[0],@row[1],@row[2], @row[3], @row[4], @row[5], @row[6])=split(/\
+s+/,$row);
if (@row[2] ne ENERGY)
{
 print  WRITE "@row[1]  $row[2]\n";
  }
    }
 }
 close(MYFILE);
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