As an aid for compiling conquest under linux, I have created a command file for using cmake (http://www.cmake.org/HTML/Index.html).
cmake is an alternative to automake and uses a single configuration file called CMakeLists.txt. Installation of cmake should be simple as binary packages are available for most linux distributions including red hat and debian based systems.
The CMakeLists.txt file plus some basic instructions are available at http://www.nmrf.org.au/conquest/conquest_cmake.html
More instructions and tips for using conquest on linux will be added as time permits.
Mark