Download file bugfix.all from the http://amber.scripps.edu/bugfixes.html into the $AMBERHOME directory and patch the Amber distribution:
cd $AMBERHOME
patch -p0 -N -r patch_rejects <bugfix.all
This should patch source files with the latest bugfixes.Before compiling Amber 9 using the Fujitsu compiler several files of the Amber distribution should be modified. To simply procedure of applying the changes to the Amber code they have been gathered in one patch file, fujitsu-fix.all. The patch should be copied to the $AMBERHOME directory and applied after applying the Amber bug fixing patch.
patch -p0 -N -r patch_rejects <fujitsu-fix.all
Before compiling the serial or parallel version of Amber one needs to place file config.h, to the $AMBERHOME/src directory.
Configuration file for serial version (shift-click or right-mouse-click for download):
Copy it in the $AMBERHOME/src directory, rename into config.h and enter
make serial
Copy it in the $AMBERHOME/src directory, rename into config.h and enter
make parallel
Copy it in the $AMBERHOME/src/pmemd/config_data directory and enter
./configure primepower_v frt nopar
make clean
make
make install
Copy it in the $AMBERHOME/src/pmemd/config_data directory and enter
./configure primepower_v frt mpi
make clean
make
make install