The Jargon File (version 4.4.7, 29 Dec 2003):

do protocol
 vi.

    [from network protocol programming] To perform an interaction with somebody
    or something that follows a clearly defined procedure. For example, ?Let's
    do protocol with the check? at a restaurant means to ask for the check,
    calculate the tip and everybody's share, collect money from everybody,
    generate change as necessary, and pay the bill. See protocol.