Tips from the Basic debugging checklist: print and Data::Dumper. This will show you that $x and $y attempt to access elements beyond the end of your @rt and @pd arrays.

What should x and y be?

I ran your code thru perltidy, then fixed some split's and cluttered it up with ugly debug code to show you how I came to those conclusions: 

use Graph::Undirected;
use warnings;
use strict;

package Graph::Base;

# Instantiate
my $G = new Graph::Undirected;

open( IN, "Input.txt" ) || die $!;

while (<IN>) {
    chomp;
    my @rxn = split /\#/, $_;

    # "$rxn[1]\n"; #debug
    my @cmp = split /\s*\<=>\s*/, $rxn[1];
#use Data::Dumper; $Data::Dumper::Sortkeys=1; print Dumper(\@cmp);

    #print"$cmp[0]\n"; # debug first element for reactants.
#    my @rt = split / \+ /, $cmp[0];    # split by space and '+'. if i
+ don't put space b/n \+ i get bad formated output.
    my @rt = split /[+\s]+/, $cmp[0];    # split by space and '+'. if 
+i don't put space b/n \+ i get bad formated output.

    my $x;                             #declaring $x b/c the use of st
+rict wouldn't allow me to $x or my ($x)!
    for ( $x = 0 ; $x <= $#rt ; $x++ ) {
        #print "$rt[$x]\n"; # debug prints the reactant compounds.
    }
#    my @pd = split /\+/, $cmp[1];
    my @pd = split /[+\s]+/, $cmp[1];
#use Data::Dumper; $Data::Dumper::Sortkeys=1; print Dumper(\@pd);
    my $y;
    for ( $y = 0 ; $y <= $#pd ; $y++ ) {
        #print "$pd[$y]\n";
    }

#use Data::Dumper; $Data::Dumper::Sortkeys=1; print Dumper(\@rt);
#use Data::Dumper; $Data::Dumper::Sortkeys=1; print Dumper(\@pd);
#print "$x $y\n";

$x=1; $y = 1;  # <----------------------------- ????????????
    $G = $G->add_edge( $rt[$x], $pd[$y] );
    print "$G\n";
}


__END__

My output:

C02=C04
C02=C04,C04=C08

[download]

Things I fixed:

In reply to Re: creating an undirected graph by toolic
in thread creating an undirected graph by filipo

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