Hey all, I am a PERL newbie trying to create a script to calculate the distance between all HIS/ASP residues and a single Zinc atom embedded into a protein. 

#!/usr/bin/perl -W

use strict;
use warnings;

#subroutines for calculations
 

sub distanceAB
{
        my $distance = 0;

        my $Ax = substr($_[0], 30, 8) + 0;
        my $Ay = substr($_[0], 38, 8) + 0;
        my $Az = substr($_[0], 46, 8) + 0;

       my $Bx = substr($_[1], 30, 8) + 0;
       my $By = substr($_[1], 38, 8) + 0;
       my $Bz = substr($_[1], 46, 8) + 0;

        $distance = sqrt(($Ax - $Bx)**2 + ($Ay - $By)**2 + ($Az - $Bz)
+**2);
        return sprintf("%4.2f", $distance);
}


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

my $input=$ARGV[0];

my $num = 0;
my $i = 0;

open IN, "<$input" or die "can't open .pdb";

my @pdblines = ();

while (<IN>) {
for ( @pdblines) {

    #chomp $pdbline;
    if (my $pdbline =~ /ZN1  LG1 X/) 
    {
        my $ZNline = $pdbline;
        next;
    }
        
    #find xyz coordinates for other atoms and store in array
    if (my $pdbline =~ /^ATOM.*(OD2 ASP|NE2 HIS)/)
    {
        
        my $Atomline = $pdbline; 
        my $resname = substr($pdbline, 16, 3);
        my $resnumber = substr($pdbline, 22, 3);
        
    #calculate Zn to each atom distance
            my $Zndistance=distanceAB(my $ZNline, $Atomline);
            if (my $Zndistance < 2.5) {
        print "$Zndistance \n";
            print "$resname $resnumber \n";
        print "Coordinator $num \n";
            }
            }        
        ++$num;
}    
}

[download]

When I run the code, I get a lot of "Use of initialized value" errors, such as

Use of uninitialized value $Znx in array element at ./getRESZNdistance.pl line 58, <IN> line 2863.

Use of uninitialized value $Znz in array element at ./getRESZNdistance.pl line 58, <IN> line 2863.

Basically when the script encounters lines that do not contain /OD2 ASP/ or /NE2 HIS/ it runs into an error from what I can see.

Any suggestions?

In reply to calculate distance between atoms and a target atom by mishimakaz

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