diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
--- amber11.orig/AmberTools/src/configure	2011-04-14 15:30:55.000000000 +0300
+++ amber11/AmberTools/src/configure	2011-06-04 12:26:45.000000000 +0300
@@ -293,7 +293,8 @@
    echo "Your AMBERHOME environment variable is not set! It should be set to"
    echo "$ambhome  NOT doing so may cause errors when you compile. Continue"
    echo "anyway? (yes or no)"
-   read answer
+   #read answer
+   answer='yes'
    if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then
       echo ""
       echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily"
@@ -356,11 +357,11 @@
 mpi_flag=
 lex=flex
 flibs_mkl=
-lapack=install
-blas=install
+lapack=skip
+blas=skip
 f2c=skip
-ucpp=install
-cpp="\$(BINDIR)/ucpp -l"
+ucpp=skip
+cpp="\$(EPREFIX)/usr/bin/ucpp -l"
 
 #-----------------------------------
 # skip building of sleap?
@@ -1655,24 +1656,24 @@
   #--------------------------------------------------------------------------
   #  Configure fftw-3.2.2:
   #--------------------------------------------------------------------------
-  if [ "$mdgx" = 'yes' ]; then
-      mdgxflag="--prefix=$AMBERHOME --disable-fortran" 
-      echo
-      echo "Configuring fftw-3.2.2 (may be time-consuming)..."
-      echo
-      cd fftw-3.2.2 && \
-      env CC="$cc" CFLAGS="$cflags $cnooptflags" \
-          ./configure $mdgxflag > ../fftw3_config.log 2>&1
-      ncerror=$?
-      if [ $ncerror -gt 0 ]; then
-          echo "    Error: FFTW configure returned $ncerror"
-          echo "    FFTW configure failed! Check the fftw3_config.log file."
-          exit 1
-      else
-          echo "    fftw-3.2.2 configure succeeded."
-      fi
-      cd ..
-  fi
+  #if [ "$mdgx" = 'yes' ]; then
+  #    mdgxflag="--prefix=$AMBERHOME --disable-fortran" 
+  #    echo
+  #    echo "Configuring fftw-3.2.2 (may be time-consuming)..."
+  #    echo
+  #    cd fftw-3.2.2 && \
+  #    env CC="$cc" CFLAGS="$cflags $cnooptflags" \
+  #        ./configure $mdgxflag > ../fftw3_config.log 2>&1
+  #    ncerror=$?
+  #    if [ $ncerror -gt 0 ]; then
+  #        echo "    Error: FFTW configure returned $ncerror"
+  #        echo "    FFTW configure failed! Check the fftw3_config.log file."
+  #        exit 1
+  #    else
+  #        echo "    fftw-3.2.2 configure succeeded."
+  #    fi
+  #    cd ..
+  #fi
 
   #--------------------------------------------------------------------------
   #  Configure python
@@ -1792,27 +1793,27 @@
           echo
           echo "Configuring fftw-2.1.5 (may be time-consuming)..."
           echo
-          cd fftw-2.1.5
-          if [ "$mpi" = 'yes' ]; then
-              ./configure $rismflag --enable-mpi \
-              CC="$cc" CFLAGS="$cflags $coptflags" \
-              F77="$fc" FFLAGS="$fflags $foptflags" \
-                  FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
-          else
-              ./configure $rismflag \
-              CC="$cc" CFLAGS="$cflags $coptflags" \
-              F77="$fc" FFLAGS="$fflags $foptflags" \
-                  FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
-          fi
-          ncerror=$?
-          if [ $ncerror -gt 0 ]; then
-              echo "    Error: fftw configure returned $ncerror"
-              echo "    fftw configure failed!  Check the fftw2_config.log file."
-              exit 1
-          else
-              echo "    fftw-2.1.5 configure succeeded."
-          fi
-          cd ..
+  #        cd fftw-2.1.5
+  #        if [ "$mpi" = 'yes' ]; then
+  #            ./configure $rismflag --enable-mpi \
+  #            CC="$cc" CFLAGS="$cflags $coptflags" \
+  #            F77="$fc" FFLAGS="$fflags $foptflags" \
+  #                FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
+  #        else
+  #            ./configure $rismflag \
+  #            CC="$cc" CFLAGS="$cflags $coptflags" \
+  #            F77="$fc" FFLAGS="$fflags $foptflags" \
+  #                FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
+  #        fi
+  #        ncerror=$?
+  #        if [ $ncerror -gt 0 ]; then
+  #            echo "    Error: fftw configure returned $ncerror"
+  #            echo "    fftw configure failed!  Check the fftw2_config.log file."
+  #            exit 1
+  #        else
+  #            echo "    fftw-2.1.5 configure succeeded."
+  #        fi
+  #        cd ..
           flibs_fftw2="-ldrfftw -ldfftw"
           if [ "$mpi" = 'yes' ]; then
               flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2"
diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at
--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at	2011-04-14 15:30:16.000000000 +0300
+++ amber11/AmberTools/src/cpptraj/src/Makefile_at	2011-05-20 00:45:48.000000000 +0300
@@ -65,8 +65,8 @@
 	-/bin/rm FindDepend.o
 	-/bin/rm findDepend
 
-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS)
-	$(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB)
+cpptraj$(SFX): $(OBJECTS)
+	$(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp
 
 $(NETCDFLIB): ../../netcdf_config.log
 	cd ../../netcdf/src && $(MAKE) install
diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile
--- amber11.orig/AmberTools/src/Makefile	2011-04-14 15:30:12.000000000 +0300
+++ amber11/AmberTools/src/Makefile	2011-05-19 23:36:36.000000000 +0300
@@ -8,15 +8,15 @@
 
 install: $(INSTALLTYPE)
 
-serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP)
+serial: configured_serial
 	@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
 #	utility routines and libraries:
-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
+#	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
 	(cd byacc && $(MAKE) install )
-	(cd arpack && $(MAKE) install );
-	(cd lapack && $(MAKE) $(LAPACK) )
-	(cd blas && $(MAKE) $(BLAS) )
-	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+#	(cd arpack && $(MAKE) install );
+#	(cd lapack && $(MAKE) $(LAPACK) )
+#	(cd blas && $(MAKE) $(BLAS) )
+#	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
 	(cd etc && $(MAKE) install )
 	(cd chamber && $(MAKE) install )
 	(cd pbsa && $(MAKE) install )
@@ -32,7 +32,7 @@
 	(cd cpptraj && $(MAKE) $(CPPTRAJ))
 
 #   miscellaneous:
-	(cd reduce && $(MAKE) install )
+#	(cd reduce && $(MAKE) install )
 
 #   leap and gleap:
 	(cd leap && $(MAKE) install )
@@ -42,7 +42,7 @@
 	(cd rism && $(MAKE) install )
 
 #   nab:
-	(cd cifparse && $(MAKE) install )
+#	(cd cifparse && $(MAKE) install )
 	(cd sff && $(MAKE) install )
 	(cd pbsa && $(MAKE) libinstall )
 	(cd nab && $(MAKE) install )
@@ -63,19 +63,19 @@
 	@echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
 	@echo ""
 
-nabonly: $(NETCDFLIB) 
+nabonly:
 #	utility routines and libraries:
-	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
+#	(cd ucpp-1.3 && $(MAKE) $(UCPP) )
 	(cd byacc && $(MAKE) install )
-	(cd arpack && $(MAKE) install );
-	(cd lapack && $(MAKE) $(LAPACK) )
-	(cd blas && $(MAKE) $(BLAS) )
-	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+#	(cd arpack && $(MAKE) install );
+#	(cd lapack && $(MAKE) $(LAPACK) )
+#	(cd blas && $(MAKE) $(BLAS) )
+#	(cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
 	(cd pbsa && $(MAKE) libinstall )
 	(cd rism && $(MAKE) install )
 
 #	nab:
-	(cd cifparse && $(MAKE) install )
+#	(cd cifparse && $(MAKE) install )
 	(cd sff && $(MAKE) install )
 	(cd nab && $(MAKE) install )
 	(cd nss && $(MAKE) install )
diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile
--- amber11.orig/AmberTools/src/mdgx/Makefile	2011-04-14 15:30:17.000000000 +0300
+++ amber11/AmberTools/src/mdgx/Makefile	2011-05-20 12:44:38.000000000 +0300
@@ -109,7 +109,7 @@
 
 FFTW_LIBS = $(LIBDIR)/libfftw3.a
 
-mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB)
+mdgx$(SFX) : $(MDGX_OBJS)
 	$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
 	-o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM)
 
diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
--- amber11.orig/AmberTools/src/pbsa/Makefile	2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/pbsa/Makefile	2011-05-19 22:27:40.000000000 +0300
@@ -148,7 +148,7 @@
 	)
 
 #---------------------------------------------------------------------------
-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial
+pbsa$(SFX): $(OBJ) syslib configured_serial
 	$(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
 	        ../lib/nxtsec.o ../lib/random.o \
 	        $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
@@ -158,7 +158,7 @@
 	        ../lib/nxtsec.o ../lib/random.o \
 	        $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
 
-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
 	$(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
 		libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \
 		$(LDFLAGS) $(AMBERLDFLAGS)
@@ -194,15 +194,15 @@
 sfflib:
 	cd ../sff && $(MAKE) install
 
-netlib: 
-	cd ../lapack && $(MAKE) $(LAPACK)
-	cd ../blas && $(MAKE) $(BLAS)
-	cd ../arpack && $(MAKE) install
-
-c9x-complex:
-	@if test $(C9XCOMPLEX) != "skip"; then \
-	   cd ../c9x-complex && $(MAKE) libmc.a; \
-	 fi
+#netlib: 
+#	cd ../lapack && $(MAKE) $(LAPACK)
+#	cd ../blas && $(MAKE) $(BLAS)
+#	cd ../arpack && $(MAKE) install
+
+#c9x-complex:
+#	@if test $(C9XCOMPLEX) != "skip"; then \
+#	   cd ../c9x-complex && $(MAKE) libmc.a; \
+#	 fi
 
 %.LIBPBSA.o: %.f
 	$(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$<
diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile
--- amber11.orig/AmberTools/src/ptraj/Makefile	2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/ptraj/Makefile	2011-05-19 23:38:36.000000000 +0300
@@ -57,25 +57,25 @@
 pubfft.o:  pubfft.f
 	$(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
 
-rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS)
+rdparm$(SFX): libs $(OBJECTS)
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
 		-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
 
-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS)
+ptraj$(SFX): libs $(OBJECTS)
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
 		-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
 
-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS)
+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS)
 	$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
 		-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
 
 libs: 
 	cd pdb && $(MAKE) 
-	cd ../arpack && $(MAKE)
+#	cd ../arpack && $(MAKE)
 
-netlib:
-	cd ../lapack && $(MAKE) $(LAPACK)
-	cd ../blas && $(MAKE) $(BLAS)
+#netlib:
+#	cd ../lapack && $(MAKE) $(LAPACK)
+#	cd ../blas && $(MAKE) $(BLAS)
 
 clean:
 	cd pdb && $(MAKE) clean
diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h
--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h	2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h	2011-05-19 22:30:43.000000000 +0300
@@ -4,7 +4,7 @@
 #    include "../../include/pnetcdf.h"
 #    define nc_strerror ncmpi_strerror
 #  else
-#    include "../../include/netcdf.h"
+#    include <netcdf.h>
 #  endif 
 #endif
 
diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h
--- amber11.orig/AmberTools/src/ptraj/ptraj.h	2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/ptraj/ptraj.h	2011-06-04 13:25:01.000000000 +0300
@@ -94,7 +94,7 @@
 #define nc_strerror ncmpi_strerror
 #include "../../include/pnetcdf.h"
 #else
-#include "../../include/netcdf.h"
+#include <netcdf.h>
 #endif
 #endif
 
diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile
--- amber11.orig/AmberTools/src/rism/Makefile	2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/rism/Makefile	2011-05-20 01:07:26.000000000 +0300
@@ -49,7 +49,7 @@
 	mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \
 	fce_c.o erfcfun.o safemem.o blend.o timer_c.o
 
-librism: $(LIBOBJ) $(FLIBS_FFTW2)
+librism: $(LIBOBJ)
 	$(AR) $(LIBDIR)/$@.a $(LIBOBJ)
 	$(RANLIB) $(LIBDIR)/$@.a
 
diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c
--- amber11.orig/AmberTools/src/sff/AmberNetcdf.c	2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/sff/AmberNetcdf.c	2011-05-20 10:49:06.000000000 +0300
@@ -27,7 +27,7 @@
 #endif
     
 #ifdef BINTRAJ
-#include "../../include/netcdf.h"
+#include <netcdf.h>
 
 #define NCFRAME "frame"
 #define NCSPATIAL "spatial"
diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile
--- amber11.orig/AmberTools/src/sff/Makefile	2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/sff/Makefile	2011-05-20 09:53:27.000000000 +0300
@@ -1,7 +1,7 @@
 include ../config.h
 
 .c.o:
-	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $<
+	$(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $<
 
 OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
 	prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \
diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
--- amber11.orig/AmberTools/src/sqm/Makefile	2011-04-14 15:30:20.000000000 +0300
+++ amber11/AmberTools/src/sqm/Makefile	2011-05-19 22:31:49.000000000 +0300
@@ -77,7 +77,7 @@
 install: sqm$(SFX)
 	mv sqm$(SFX) $(BINDIR)
 
-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
 	$(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
 		$(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
 
@@ -94,10 +94,10 @@
 sys:
 	cd ../lib; $(MAKE) sys.a
 
-netlib:
-	cd ../lapack; $(MAKE) $(LAPACK)
-	cd ../blas; $(MAKE) $(BLAS)
-	cd ../arpack && $(MAKE) install
+#netlib:
+#	cd ../lapack; $(MAKE) $(LAPACK)
+#	cd ../blas; $(MAKE) $(BLAS)
+#	cd ../arpack && $(MAKE) install
 
 clean:
 	/bin/rm -f *.o _*.f *.mod *.d sqm$(SFX)