The error you get comes from the fact that you need to quote djn-geo, as it doesn't look like a bareword to Perl.
That said there are many other problems with your code. I suspect what you want is something like this (untested):
#!/usr/bin/perl
use strict;
use warnings;
use XML::Twig;
# get the user input. die if it doesn't look right
my $enter = <STDIN>;
my @fields = split(/ /, $enter);
if( @fields != 2) { die "usage $0 <input_file> <output_file>\n"; }
# no need to open the file, quote djn-geo
my $t= XML::Twig->new( twig_roots => { 'djn-geo' => 1});
$t->parsefile($fields[0]);
# print_to_file was added in XML::Twig 3.23
$twig->print_to_file( $fields[1]);