There might be limitations that prevent you from installing Messaging Server against a Directory Server master:
You do not have Directory Server master credentials.
Messaging Server cannot communicate directly with the Directory Server master.
Run the comm_dssetup.pl program against all Directory Servers including the Directory Server replicas as noted in comm_dssetup.pl Requirements.
Run the Messaging configure program using the replicated Directory Server credentials as described in Creating the Initial Messaging Server Runtime Configuration.
By default, this program is located in msg_svr_base/sbin/configure.
Because of invalid privileges, the configure program will fail in trying to configure the Directory Server Administrators. It will, however, produce the msg_svr_base/config/*.ldif files that are needed to allow proper privileges to the Directory Server replicas.
Move the *.ldif files to the Directory Server master.
Run the ldapmodify command on the *.ldif files.
See the Sun Java System Directory Server documentation for more information on ldapmodify or in the msg_svr_base/install/configure_YYYYMMDDHHMMSS.log.
Run the configure program again.
Your Directory Server replica (and master) are now configured to work with your Messaging Server.