I don't have time to go into details, but to complete the obsolete style you are using, you would do

local (*Axcoord, *Aycoord, *Azcoord, *Bxcoord, *Bycoord, *Bzcoord, *re
+s_to_atom, *natres, $nseg, *beginning, *ending) = @_;

our @Axcord;
our @Aycord;
our @Azcord;
our @Bxcord;
our @Bycord;
our @Bzcord;

...
$Axcord[$counter]
...
[download]

Better way:

my ($Axcoord, $Aycoord, $Azcoord, $Bxcoord, $Bycoord, $Bzcoord, $res_t
+o_atom, $natres, $nseg, $beginning, $ending) = @_;

...
$Axcord->[$counter]
...
[download]

Update: I thought I aborted posting this message. It's obviously overly rushed for the amount of problems in the OP.