Name "main::ZNx" used only once: possible typo at ....
Name "main::Znz" used only once: possible typo at ....
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Also, you probably want to change:

if ($pdbline =~ /OD2 ASP/ or /NE2 HIS/)
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to:

if ($pdbline =~ /OD2 ASP/ or $pdbline =~ /NE2 HIS/)
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yeah, toolic gave a better recommendation :)

Don't use this sort of construct:

You are testing 2 possibilities here. The first one is $pdbline =~ /OD2 ASP/ which may be fine, but the second one is /NE2 HIS/ which by default will test $_ which is probably not what you want. Either combine the 2 regular expressions into 1 (left as an exercise) or test them individually like this:

The "Use of uninitialized value" reports you see are warnings, not errors. However, the fact that they are presented to you indicates that you are attempting to do something with an uninitialised value which is usually not what you intend.

In this specific case, your references to items like $x1[$Znx] on line 58 will give that if the $Znx is uninitialised. You will need to trace through the logic to see how that might happen and correct it.

Best advice is:

• use strict; # Always
• Lose the prototypes unless you have a very, very good reason for keeping them.
• Don't use "or" like you were.

Best of luck with the rest of it.

if (X) {
    $Znx = ...;
} elsif (Y) {
    $Znx = ...;
}
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my $pdbline = <IN>;
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my $filename = $ARGV[0];
open(my $fh, '<:encoding(UTF-8)', $filename)); 
while (my $pdbline = <$fh>) {
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Secondly, regular expressions offer a convenient method to capture specific parts of input. This allows one to write, e.g. @Zn = ($1, $2, $3); — but you must include (...) groups in the pattern. If the data is of rigidly fixed format, pack() and unpack() are often quite useful:

my $xyz_fmt = '@30a7 @38a6 @46a6';
while ($pdbline = <IN>) {
    if ($pdbline =~ m/ZN1  LG1 X/) 
    {
        @Zn = unpack $xyz_fmt, $pdbline;
        next;
    }
    if ($pdbline =~ /^ATOM.*(OD2 ASP|NE2 HIS)/)
    {
        push @Atoms, [unpack $xyz_fmt, $pdbline];
        ...
    }
}
# ... do the calculations once we have all data.
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Update: for questions regarding the handling of AoA, please see perllol or perldsc.

I am trying to use your suggestion, but also at the same time, create an array of "Atoms" such that I can calculate the distance between the Zinc atom and all other OD2 and NE2 atoms. So I am trying to use ++$num to tally up the number of OD2s and NE2s It would appear that the problem is in the this line

push $Atoms$num, unpack $xyz_fmt, $pdbline;

#!/usr/bin/perl -W


#subroutines for calculations

use strict;

sub distanceAB($$$$$$) {
    my ($x1,$y1,$z1,$x2,$y2,$z2) = @_;
    $distance = sqrt (($x2-$x1)**2 + ($y2 -$y1)**2 + ($z2-$z1)**2);
    return sprintf("%4.2f", $distance);
    }

#open files for calculations and modify distance cutoff for target res
+idues

$input=$ARGV[0];

open(IN, "$input");

$num = 0;
$count = 0; 

my $xyz_fmt = '@30a8 @38a8 @46a8';

while ($pdbline = <IN>) {
    if ($pdbline =~ m/ZN1  LG1 X/) 
    {
        @ZN = unpack $xyz_fmt, $pdbline;
        next;
    }
        
    #find xyz coordinates for other atoms and store in array
    if ($pdbline =~ /^ATOM.*(OD2 ASP|NE2 HIS)/)
    {
        push $Atoms[$num], [unpack $xyz_fmt, $pdbline]; 
        $resname[$num] = substr($pdbline, 16, 3);
        $resnumber[$num] = substr($pdbline, 22, 3);
            
        ++$num;
        }
    }        

#count number of potential coordinating atoms
    if ($pdbline =~ /OD2 ASP/ or $pdbline =~ /NE2 HIS/)    {
        ++$count;
    }
        
    #calculate Zn to each atom distance
    foreach $i (0..$count) {
    $Zndistance=distanceAB($x1[$ZN[0]],$y1[$ZN[1]],$z1[$ZN[2]],$x2[$At
+oms[$i][0]],$y2[$Atoms[$i][1]],$z2[$Atoms[$i][2]]);
    if ($Zndistance < 2.5) {
    $distanceAB=$Zndistance;
    print "$distanceAB \n";
    print "$resname[$i] $resnumber[$i] \n";
    }
    }
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Regarding my new code, how would I implement my subroutine calculation?

they do in a PDB file, its a snapshot of a protein structure, not an accurate representation but the best we have in most cases



This is not a Signature...

You'd need to post the updated code if you are to get help with it.

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My mistake. I updated my original post instead of pasting the code onto another post.