3.3. Building of Amber/APBS module

Currently the Amber/APBS module is supported on i386 and x86_64 Linux platforms only. The Intel compiler is recommended.

1. Amber9 source code must be first patched for use with iAPBS. No patching is necessary for Amber10.

   Amber9:

   export APBS_LIB=${APBS_PREFIX}/lib cd $AMBERHOME/src ./configure ifort_ia32 cd $AMBERHOME/src/sander make clean cp ${APBS_PREFIX}/iapbs-1.0.0/modules/Amber/apbs.f90 ./apbs.f cp ${APBS_PREFIX}/iapbs-1.0.0/modules/Amber/apbs_vars.f90 ./apbs_vars.f patch -b -z .orig -p1 < \ ${APBS_PREFIX}/iapbs-1.0.0/modules/Amber/patches/amber9_sander.patch make depend unset CC F77 unset CFLAGS FFLAGS LDFLAGS

   Amber10:

   export APBS_LIB=${APBS_PREFIX}/lib cd $AMBERHOME/src ./configure_at icc ./configure_amber ifort cd $AMBERHOME/src/sander make clean make depend unset CC F77 unset CFLAGS FFLAGS LDFLAGS

2. After this, the sander source code is ready for building and linking with iAPBS:

   make -e AMBERBUILDFLAGS="-DAPBS" sander.APBS

   After this last step the directory $AMBERHOME/src/sander should contain sander.APBS executable.

3. To verify that the built binary produces correct results run tests in $AMBERHOME/test directory:

   export TESTsander=${AMBERHOME}/src/sander/sander.APBS cd ${AMBERHOME}/test/iapbs_radi ./Run.ion.min