To build you must go to the cudpp directory in trunk, you must then modify
linux_build/common.mk and common/common.mk and replace CUDA_INSTALL_PATH 
within the file with your cuda install path. Then enter the cudpp directory
and type make, once that has finished enter the common directory and type make.

You must then copy the two files in the lib directory to 
openmm/platforms/cuda/cudpp/linux for a 32bit linux install and 
openmm/platforms/cuda/cudpp/linux64 for a 64bit install. 

You must also make sure that the cudpp library is called libcudpp.a and not
libcudpp64.a as it is build on a 64bit machine.