I suppose that you need a virtualised Domino server, and that you do not want to copy the entire server+O/S to a virtual system. If that is the case:
- set up the VM and install the O/S
- install Domino, but don't set it up
- shut down the running Domino server, but leave the server on
- copy/move the entire Domino data tree from the old server to the virtual one
- copy all additional S/W to the virtual server (Externsion Manager stuff, etc.)
- now shutdown the old server or give it a different DNS-name and/or IP-address
- make sure the virtual server has the same credentials as the old server (IP-address)
- start the Domino server
This way, you can even move from a Windows server to a Linux server.
Users shouldn't even be aware of the difference.