Why do you want to do that? ISPConfig contains dkim signing and that is done by amavisd, opendkim is not required, if you would install opendkim, then dkim support in ispconfig will stop working.
remove open-dkim and update to the latest ispconfig and choose "reconfigure services" during the update.
If you followed the perfect-setup everything is installed. ISPConfig uses amvis to sign mails with dkim. Did you choose reconfigure services during the update? You can debug dkim: http://blog.schaal-24.de/dkim/debug-2/?lang=en