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
Configuration for Intel C Compiler with MPI
To compile DOCK with icc in parallel, add the file below as intel.parallel to your dock6/install directory.
CC= icc CXX= $(MPICH_HOME)/bin/mpicxx CFLAGS= -O3 -ipo -fast -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I$(MPICH_HOME)/include FC= ifort FFLAGS= -O2 LIBS= -L$(MKL_HOME)/lib/em64t -lvml -lmkl_lapack -lmkl -lguide -lpthread -lm LIBS= $(MKL) LINK_WITHOUT_FORTRAN_MAIN= -nofor_main LOAD= $(MPICH_HOME)/bin/mpicxx DOCK_SUFFIX= .mpi AR= ar rv LEX= flex OCFLAGS= -O3 -D_ANSI_SOURCE RANLIB= ranlib