There are many things that don't need to happen, and you haven't shown them to us:

    for ($iseg = 1; $iseg <= $nseg; $iseg++){
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For example, $nseg might be zero, undef or a negative number or some string.

    for ($ires = $beginning[$iseg]; $ires <= $ending[$iseg]; $ires++) 
+{
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@ending might be empty or contain values numerically smaller than @beginning.

                if ($ires == $interdomainatoms[$counter]) {
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The same counts for @interdomainatoms.

You don't consider all these to be important, because you haven't shown them to us. So it must be something else that is not in the code you've shown at all. Maybe STDOUT is closed?

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.

Besides what the previous posters have stated, have you said:

  use strict;
  use warnings;
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at the top of your perl code?

Hello Everyone, I've included data in the example now and used strict and warnings, but I'm still not able to enter the if conditional; can anyone eluminate why this might be happening please?! many thanks in advance Dan

#!C:\Perl\bin

use strict;
use warnings;

my @beginning = (34, 76);
my @ending = (72, 85);
my @interdomainatoms = (33, 34, 72, 73, 75, 76, 77, 78);
my $jcounter = 0;
my $nseg = 1;

    for (my $iseg = 0; $iseg <= $nseg; $iseg++){

        for (my $ires = $beginning[$iseg]; $ires <= $ending[$iseg]; $i
+res++) {

                if ($ires == $interdomainatoms[$jcounter]) {

                print STDOUT $ires;

                $jcounter++;
                }    
           }    
    }
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I'm still not able to enter the if conditional

It's no surprise since the first element in @interdomainatoms, 33, is not inside any ranges you defined.

Just guessing, as still some code seems missing: add another loop for $jcounter to check all @interdomainatoms. There are still places for optimisation, but first the code must work.