For the AMS 536 class, DOCK is already installed. This article is for users trying to install dock elsewhere. Please note that DOCK is licensed software; please contact UCSF for a license. DOCK licenses are free for academic users.
Installing DOCK 6.3 on Ubuntu
These should also work for other versions of DOCK.
apt-get install build-essential flex bison gfortran cd dock6/src/install
Edit the gnu profile to replace g77 with gfortran as directed
./configure gnu make install