On May 5th 2004, Eric Pettersen wrote:

As for MatchMaker, right now it is too closely tied to the GUI dialog to be called from nogui mode. I will work on disassociating the underlying computation from the graphical interface so that it can become a command-line command. The hydrogen-bond finder has recently been given this kind of treatment and is callable from the command line in the release we will be making later this week. I'll send mail when the same is true for MatchMaker.

The command-line version of MatchMaker will be in our upcoming release-candidate snapshot, which will be out at the end of this week. --Eric