#     Open each PDB
      foreach my $pdb_file (<$pdb_list>) {
         {  
            chomp($pdb_file);
            my $tmp_file; # We would open the PDB with this handle
            open($tmp_file, "< $pdb_file") or (die "Cannot open PDB: $!");

#           Read X,Y,Z coordinates
            my @X; # X-coordinates
            my @Y; # Y-coordinates
            my @Z; # Z-coordinates
            my @pdb_tmp=<$tmp_file>;
            foreach (@pdb_tmp) {
               if (substr($_,0,3) eq "ATO") {
                  push @X, substr($_,30,8);
                  push @Y, substr($_,38,8);
                  push @Z, substr($_,46,8);
               }
            }

#           Find the interaction pairs. Also strore the best angle, should it
#           occur again with another proton. Also keep track of the waters
#           that have made h-bond with the solute atoms.
            my @sel_wat;  # Array of water molecule (numbers) selected
            my %hbond;    # $hbond[$tag1:$tag2][0]=distance
                          # $hbond[$tag1:$tag2][0]=angle

#           Solute as donor and water as acceptor
            {
               my @atom_cov; # Polar solute atom that is already covered.
               for (my $i=0; $i <= $#pol_h; $i++) {
#                 If this donor is not already covered, then go ahead.
                  if ( ! defined($atom_cov[$pol_h[$i][1]]) ) {
                     for (my $j=0; $j <= $#wat_a; $j++) {
                        my $dx=$X[$pol_h[$i][1]]-$X[$wat_a[$j]];
                        my $dy=$Y[$pol_h[$i][1]]-$Y[$wat_a[$j]];
                        my $dz=$Z[$pol_h[$i][1]]-$Z[$wat_a[$j]];

                        my $distSq=($dx*$dx)+($dy*$dy)+($dz*$dz);
                        if ($distSq <= $hb_dist) {
                           $atom_cov[$pol_h[$i][1]]=1;
                           print $idty[$pol_h[$i][1]], " ", 
                                 $idty[$wat_a[$j]], $distSq,"\n";
                        }
                     }
                  }
               }
            }
         }
      }