There are several settings related to that limit. You may wish to modify the following to suit your needs and paste it into the "Apache directives" box for the site:
php_admin_value memory_limit 1024M
php_admin_value max_execution_time 0
php_admin_value max_input_time 0
php_admin_value post_max_size 2000M
php_admin_value file_uploads On
php_admin_value upload_max_filesize 2000M
php_admin_value session.cookie_lifetime 0
php_admin_value session.gc_maxlifetime 259200
Give it about 5 minutes for ISPConfig to refresh the directives, and see if your script functions as expected.
Note also that you may use the phpinfo() function in a script that resides within the same directory as the script you are testing to confirm that the directives are being applied.
Finally, the values in the example above are quite large; you may have no need to use such large values in your particular case.