With what you've provided, no. See How (Not) To Ask A Question. Specifically, without knowing what is in your arrays (@beginning, @ending, @interdomainatoms) there is no way replicate your code's behavior.

As a stylistic note which has nothing to do with your present query, using foreach loops in place of C-style for loops will make your code less prone to typographical bugs, e.g.

my $counter = 1;

foreach my $iseg (1 .. $nseg){
    foreach my $ires ($beginning[$iseg] .. $ending[$iseg]) {
        if ($ires == $interdomainatoms[$counter]) {
            print STDOUT $interdomainatoms[$counter];                
            $counter++;
        }        
    }
}
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See For Loops for details.