Hi, I am creating a program that calculates the distance between the x, y, z coordinates of atoms listed in a pdb file. So far i have this : 
#!/usr/bin/perl -w


$num = 0;
$count = 0;

while (<>) {  

# Find x, y, z coordinates and store in separate arrays

    if ($_ =~ /^ATOM/) {
        @line = $_ =~ m/^(.....).(.....).(....).(...)..(....)....(....
+....)(........)(........)/;
        
        $x = $line[5];
        $arrayx[$num] = $x;
                         
        $y = $line[6];
        $arrayy[$num] = $y;
        
        $z = $line[7];
        $arrayz[$num] = $z;
        
        ++$num;        
    }    

# Count number of atoms
    
    if ($_ =~ /^ATOM/) {
        ++$count;
    }
}

# Calculate distance between all atom coordinates

foreach $i (0..$count) {

    foreach $j ($i + 1..$count) {
    
    $dist = sqrt(
            ($arrayx[$i] - $arrayx[$j])**2 +
            ($arrayy[$i] - $arrayy[$j])**2 +
            ($arrayz[$i] - $arrayz[$j])**2
        );
    
    print "$dist\n";
    
    }
}

[download]
When I run the program i get this message popping up for some of the lines and I don't know what to do to fix it: "Use of uninitialized value in subtraction (-) at ./gas.pl line 42, <> line 14368" The line that it states is the last line of the pdb file, however i don't see why this line is involved in my calculations as this is not present in any of my arrays. The pdb file I'm using is 3PBL.pdb (sorry wasn't able to attach or post link but easy to find if u put that name into google). Any help would be much appreciated as I am VERY new to Perl. Thanks

In reply to Calc distance between atoms in pdb file by stellaparallax

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