Haha!! thats a lot of money!! Actually have tried to get some part of it ...

use strict;

my @pdb=();
my @atoms;

open(IN, "/home/subs/vindytest/PDB.pl") or die "Could not open file!";

while (my $line = <IN>) {

my @array = (split (/\s+/, $line))[6, 7, 8];

print ("@array\n");

push @pdb,[@array] ;

}
close (IN);

for my $i1 ( 0 .. $#pdb-1 ){
my ( $x1, $y1, $z1 ) = @{ $pdb[$i1] };

for my $i2 ( 1 .. $#pdb ){
my ( $x2, $y2, $z2 ) = @{ $pdb[$i2] };
my $dist = sqrt( ($x2-$x1)**2 + ($y2-$y1)**2 + ($z2-$z1)**2 );
print "distance from ( $x1, $y1, $z1 ) to ( $x2, $y2, $z2 ) is $dist\n";
}
}

Im completely stuck when it comes to picking all the elements in a row from file A and B ... i mean since i am picking from 6,7,8 only.. also the output should have all the details... Im new to perl and just so lost!! Any help would be really appreciated