More updates and fixes

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key F82F92E6)

6 files changed, 316 insertions, 172 deletions

diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
index 12620c0d9..a70bb35f8 100644
--- a/sci-chemistry/ambertools/Manifest
+++ b/sci-chemistry/ambertools/Manifest
@@ -1,26 +1,24 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA256
 
-AUX 1.4-Makefile.patch 1046 RMD160 be42d01ac81905cd05ada068a342b0ac246c40ee SHA1 0211515b502fbd6620fe0cd163001dbc50cd5f87 SHA256 2639941b0eda0e84d2cbad4ec46e316de2cc97bc691dbbe72a82664f39428a6b
-AUX 1.4-configure-fftw.patch 3508 RMD160 b6c1df7837c969833e3789f4ad88edc99ff48918 SHA1 4800f9a43e74b1aca225e0764d8f58b7bb3db673 SHA256 6e720582d71b4ddac416e663f844a054645276e3b6ea2ab0177b008d95015880
-AUX 1.4-configure.patch 597 RMD160 751ca2694058bd75b6a511e53005e9cf42d82116 SHA1 7e3cee71a0b4a5a923193298738712944d6de028 SHA256 25783608e8b4c273e548977c561d235341f041277d4395aeb7cb6fa78e06586a
+AUX ambertools-1.4-gentoo.patch 9926 RMD160 d84b121e1fa940cbf949855de3a5f0bee7566330 SHA1 08ea41b969bed5320230420d047e71a28333f76c SHA256 8f520c01146a704173ca31c68dc9440e2938263416f6d0c95de22d138426e01f
 DIST AmberTools-1.4.tar.bz2 67331137 RMD160 b499e18b583a0b454dd3a554986c19c111822e6a SHA1 ef0f9a44c8767ed35f942fd41afc636b67da0389 SHA256 af61da2f3643b4ec7f41620242b734a3cb4a79c5d422100fbd1fd1c402fecfc1
-EBUILD ambertools-1.4.ebuild 2368 RMD160 a39a4442113583e661780105a07709aa9921e2c8 SHA1 8c7fa204a8e5a12a529b9ab106651a3a76779e57 SHA256 d8679a8dfdc5e1471ca6a93f04e4787e678aca7a51b3e5beb6cac570734f4bd5
+EBUILD ambertools-1.4.ebuild 2371 RMD160 77e80c4dc3338b4a24fd32a27a1b1ab1c06e11e9 SHA1 07daeddb4bec0b2414bcf06f2b734838a66dcaa7 SHA256 ed75a35dd1eb513b1bc8f2f04797efd46609f020f979e074683b4f825d80c7cb
 MISC metadata.xml 263 RMD160 9484584cc295931e963dc785e211261f68e48c82 SHA1 a2c5af57c8eb879a4249fc0240432a4fc5b91ca5 SHA256 0e94df6d8502bc41ccd18ec4d570490e245c08595e837fd116a255458939e69b
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diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild
index 2ba836c27..d5fb35be8 100644
--- a/sci-chemistry/ambertools/ambertools-1.4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.4.ebuild
@@ -15,12 +15,13 @@ SRC_URI="AmberTools-${PV}.tar.bz2"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="mpi openmp lapack X"
+IUSE="mpi openmp X"
 RESTRICT="fetch"
 
 RDEPEND="
 	virtual/cblas
 	virtual/lapack
+	sci-libs/arpack
 	sci-libs/cifparse-obj
 	sci-chemistry/mopac7
 	sci-libs/netcdf
@@ -51,34 +52,33 @@ pkg_setup() {
 }
 
 src_prepare() {
-	epatch "${FILESDIR}/${PV}-configure.patch"
-	epatch "${FILESDIR}/${PV}-configure-fftw.patch"
-	epatch "${FILESDIR}/${PV}-Makefile.patch"
+	epatch "${FILESDIR}/${P}-gentoo.patch"
 	cd AmberTools/src
-	rm -r byacc c9x-complex cifparse netcdf reduce ucpp-1.3 || die
+	rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
 }
 
 src_configure() {
 	cd AmberTools/src
-	sed -e "s:\\\\\$(LIBDIR)/arpack.a:/usr/$(get_libdir)/libarpack.a:g" \
-		-e "s:\\\\\$(LIBDIR)/lapack.a:/usr/$(get_libdir)/libclapack.a:g" \
-		-e "s:\\\\\$(LIBDIR)/blas.a:/usr/$(get_libdir)/libcblas.a:g" \
+	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
 		-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
 		-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
 		-e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
 		-e "s:fc=g77:fc=${FORTRANC}:g" \
-		-e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=/usr/$(get_libdir)/libnetcdf.a:g" \
+		-e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=$(pkg-config netcdf --libs):g" \
 		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
 		-e "s:-O3::g" \
 		-i configure
-#		-e "s:\\\\\$(LIBDIR)/f2c.a:/usr/$(get_libdir)/libf2c.a:g" \
 
 	local myconf
 
 	use X || myconf="${myconf} -noX11"
 
-	for x in mpi openmp lapack; do
-		use ${x} && myconf="${myconf/lapack/scalapack} -${x}"
+	for x in mpi openmp; do
+		use ${x} && myconf="${myconf} -${x}"
 	done
 
 	./configure \
diff --git a/sci-chemistry/ambertools/files/1.4-Makefile.patch b/sci-chemistry/ambertools/files/1.4-Makefile.patch
deleted file mode 100644
index 7a893e6c5..000000000
--- a/sci-chemistry/ambertools/files/1.4-Makefile.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- amber11/AmberTools/src/Makefile.orig	2011-03-07 00:08:41.000000000 +0300
-+++ amber11/AmberTools/src/Makefile	2011-03-07 00:10:01.000000000 +0300
-@@ -11,12 +11,12 @@
- serial: configured_serial $(NETCDFLIB)
- 	@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
- #	utility routines and libraries:
--	(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 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 etc && $(MAKE) install )
- 	(cd chamber && $(MAKE) install )
- 	(cd pbsa && $(MAKE) install )
-@@ -30,7 +30,7 @@
- 	(cd ptraj && $(MAKE) install )
- 
- #   miscellaneous:
--	(cd reduce && $(MAKE) install )
-+#	(cd reduce && $(MAKE) install )
- 
- #   leap and gleap:
- 	(cd leap && $(MAKE) install )
diff --git a/sci-chemistry/ambertools/files/1.4-configure-fftw.patch b/sci-chemistry/ambertools/files/1.4-configure-fftw.patch
deleted file mode 100644
index b91f0fcf1..000000000
--- a/sci-chemistry/ambertools/files/1.4-configure-fftw.patch
+++ /dev/null
@@ -1,86 +0,0 @@
---- amber11/AmberTools/src/configure.orig	2011-03-07 00:28:56.000000000 +0300
-+++ amber11/AmberTools/src/configure	2011-03-07 00:30:55.000000000 +0300
-@@ -1241,24 +1241,24 @@
-   #--------------------------------------------------------------------------
-   #  Configure fftw-3.2.2:
-   #--------------------------------------------------------------------------
--  if [ "$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" ./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" ./configure $mdgxflag \
-+  #            > ../fftw3_config.log 2>&1
-+  #    ncerror=$?
-+  #    if [ $ncerror -gt 0 ]; then
-+  #        echo "    Error: fftw configure returned $ncerror"
-+  #        echo "    fftw configure failed!  Check the fftw3_config.log file."
-+  #        exit 1
-+  #    else
-+  #        echo "    fftw-3.2.2 configure succeeded."
-+  #    fi
-+  #    cd ..
-+  #fi
- 
-   #--------------------------------------------------------------------------
-   #  Set up MPI 3D-RISM in NAB and SANDER
-@@ -1307,23 +1307,23 @@
-           echo
-           echo "Configuring fftw-2.1.5; (may be time-consuming)"
-           echo
--          cd fftw-2.1.5
--          if [ "$mpi" = 'yes' ]; then
--              ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
--                  > ../fftw2_config.log 2>&1
--          else
--              ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
--                  > ../fftw2_config.log 2>&1
--          fi
--          ncerror=$?
--          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="$cflags" F77="$fc" FFLAGS="$fflags" \
-+ #                 > ../fftw2_config.log 2>&1
-+ #         else
-+ #             ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
-+ #                 > ../fftw2_config.log 2>&1
-+ #         fi
-+ #         ncerror=$?
-+ #         if [ $ncerror -gt 0 ]; then
-+ #             echo "    Error: fftw configure returned $ncerror"
-+ #             echo "    fftw configure failed!  Check the fftw2_config.log file."
-+ #             exit 1
-+ #         else
-+ #             echo "    fftw-2.1.5 configure succeeded."
-+ #         fi
-+ #         cd ..
-           flibs_fftw2="\$(LIBDIR)/libdrfftw.a \$(LIBDIR)/libdfftw.a"
-           if [ "$mpi" = 'yes' ]; then
-               flibs_fftw2="\$(LIBDIR)/libdrfftw_mpi.a \$(LIBDIR)/libdfftw_mpi.a $flibs_fftw2"
diff --git a/sci-chemistry/ambertools/files/1.4-configure.patch b/sci-chemistry/ambertools/files/1.4-configure.patch
deleted file mode 100644
index ce5377eb2..000000000
--- a/sci-chemistry/ambertools/files/1.4-configure.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- amber11/AmberTools/src/configure.orig	2011-03-07 00:05:24.000000000 +0300
-+++ amber11/AmberTools/src/configure	2011-03-07 00:07:59.000000000 +0300
-@@ -288,11 +288,11 @@
- mpi_flag=
- lex=flex
- flibs_mkl=
--lapack=install
--blas=install
-+lapack=skip
-+blas=skip
- f2c=skip
--ucpp=install
--cpp="\$(BINDIR)/ucpp -l"
-+ucpp=skip
-+cpp="\$(EPREFIX)/usr/bin/ucpp -l"
- 
- #-----------------------------------
- # skip building of sleap?
-@@ -1451,7 +1451,7 @@
- LDFLAGS=$ldflags \$(AMBERBUILDFLAGS)
- 
- LEX=   $lex
--YACC=  \$(BINDIR)/yacc
-+YACC=  \$(EPREFIX)/usr/bin/yacc
- AR=    ar rv
- M4=    $m4
- RANLIB=$ranlib
diff --git a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch
new file mode 100644
index 000000000..c067928cb
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch
@@ -0,0 +1,289 @@
+diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
+--- amber11.orig/AmberTools/src/configure	2010-04-23 18:17:17.000000000 +0400
++++ amber11/AmberTools/src/configure	2011-03-07 03:39:14.000000000 +0300
+@@ -288,11 +288,11 @@
+ 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?
+@@ -1241,24 +1241,24 @@
+   #--------------------------------------------------------------------------
+   #  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" ./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" ./configure $mdgxflag \
++  #            > ../fftw3_config.log 2>&1
++  #    ncerror=$?
++  #    if [ $ncerror -gt 0 ]; then
++  #        echo "    Error: fftw configure returned $ncerror"
++  #        echo "    fftw configure failed!  Check the fftw3_config.log file."
++  #        exit 1
++  #    else
++  #        echo "    fftw-3.2.2 configure succeeded."
++  #    fi
++  #    cd ..
++  #fi
+ 
+   #--------------------------------------------------------------------------
+   #  Set up MPI 3D-RISM in NAB and SANDER
+@@ -1307,23 +1307,23 @@
+           echo
+           echo "Configuring fftw-2.1.5; (may be time-consuming)"
+           echo
+-          cd fftw-2.1.5
+-          if [ "$mpi" = 'yes' ]; then
+-              ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
+-                  > ../fftw2_config.log 2>&1
+-          else
+-              ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
+-                  > ../fftw2_config.log 2>&1
+-          fi
+-          ncerror=$?
+-          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="$cflags" F77="$fc" FFLAGS="$fflags" \
++ #                 > ../fftw2_config.log 2>&1
++ #         else
++ #             ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \
++ #                 > ../fftw2_config.log 2>&1
++ #         fi
++ #         ncerror=$?
++ #         if [ $ncerror -gt 0 ]; then
++ #             echo "    Error: fftw configure returned $ncerror"
++ #             echo "    fftw configure failed!  Check the fftw2_config.log file."
++ #             exit 1
++ #         else
++ #             echo "    fftw-2.1.5 configure succeeded."
++ #         fi
++ #         cd ..
+           flibs_fftw2="\$(LIBDIR)/libdrfftw.a \$(LIBDIR)/libdfftw.a"
+           if [ "$mpi" = 'yes' ]; then
+               flibs_fftw2="\$(LIBDIR)/libdrfftw_mpi.a \$(LIBDIR)/libdfftw_mpi.a $flibs_fftw2"
+diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile
+--- amber11.orig/AmberTools/src/Makefile	2010-04-14 17:36:31.000000000 +0400
++++ amber11/AmberTools/src/Makefile	2011-03-07 03:39:38.000000000 +0300
+@@ -8,15 +8,15 @@
+ 
+ install: serial
+ 
+-serial: configured_serial $(NETCDFLIB)
++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 )
+@@ -30,14 +30,14 @@
+ 	(cd ptraj && $(MAKE) install )
+ 
+ #   miscellaneous:
+-	(cd reduce && $(MAKE) install )
++#	(cd reduce && $(MAKE) install )
+ 
+ #   leap and gleap:
+ 	(cd leap && $(MAKE) install )
+ 	(cd gleap && $(MAKE) install )
+ 
+ #	nab:
+-	(cd cifparse && $(MAKE) install )
++#	(cd cifparse && $(MAKE) install )
+ 	(cd nab && $(MAKE) install )
+ 	(cd nss && $(MAKE) install )
+ 
+@@ -50,15 +50,15 @@
+ 
+ nabonly: $(NETCDFLIB) 
+ #	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) )
+ 
+ #	nab:
+-	(cd cifparse && $(MAKE) install )
++#	(cd cifparse && $(MAKE) install )
+ 	(cd nab && $(MAKE) install )
+ 	(cd nss && $(MAKE) install )
+ 
+diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
+--- amber11.orig/AmberTools/src/pbsa/Makefile	2010-04-14 17:26:17.000000000 +0400
++++ amber11/AmberTools/src/pbsa/Makefile	2011-03-07 03:39:15.000000000 +0300
+@@ -47,10 +47,10 @@
+ 	$(LIBDIR)/libpbsa.a $(LIBDIR)/libFpbsa.a
+ 
+ #---------------------------------------------------------------------------
+-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex
++pbsa$(SFX): $(OBJ) syslib
+ 	$(FC) -o pbsa$(SFX) $(OBJ) ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS)
+ 
+-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
++simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
+ 	$(FC) -o simplepbsa$(SFX) simplepbsa.o gopt.o libpbsa.a \
+ 	$(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS)
+ 	/bin/mv simplepbsa$(SFX) $(BINDIR)
+@@ -76,15 +76,15 @@
+ 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) -DLIBPBSA $< > _$<
+diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile
+--- amber11.orig/AmberTools/src/ptraj/Makefile	2010-03-31 07:05:16.000000000 +0400
++++ amber11/AmberTools/src/ptraj/Makefile	2011-03-07 03:39:16.000000000 +0300
+@@ -60,20 +60,20 @@
+ rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS)
+ 	$(CC) $(LDFLAGS) -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+ 
+-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS)
++ptraj$(SFX): libs $(NETCDFLIB) $(OBJECTS)
+ 	$(CC) $(LDFLAGS) -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
+ 
+-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS)
++ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS)
+ 	$(CC) $(LDFLAGS) -o ptraj.MPI$(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; $(MAKE) clean
+diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h
+--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h	2010-03-31 07:05:16.000000000 +0400
++++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h	2011-03-07 03:39:17.000000000 +0300
+@@ -4,7 +4,7 @@
+ #    include "../pnetcdf/include/pnetcdf.h"
+ #    define nc_strerror ncmpi_strerror
+ #  else
+-#    include "../netcdf/include/netcdf.h"
++#    include <netcdf.h>
+ #  endif 
+ #endif
+ 
+diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h
+--- amber11.orig/AmberTools/src/ptraj/ptraj.h	2010-03-31 07:05:16.000000000 +0400
++++ amber11/AmberTools/src/ptraj/ptraj.h	2011-03-07 03:39:17.000000000 +0300
+@@ -94,7 +94,7 @@
+ #define nc_strerror ncmpi_strerror
+ #include "../pnetcdf/include/pnetcdf.h"
+ #else
+-#include "../netcdf/include/netcdf.h"
++#include <netcdf.h>
+ #endif
+ #endif
+ 
+diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
+--- amber11.orig/AmberTools/src/sqm/Makefile	2010-04-14 16:13:28.000000000 +0400
++++ amber11/AmberTools/src/sqm/Makefile	2011-03-07 03:39:17.000000000 +0300
+@@ -77,7 +77,7 @@
+ install: sqm$(SFX)
+ 	mv sqm$(SFX) $(BINDIR)
+ 
+-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
++sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
+ 	$(FC) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) $(FLIBSF) ../lib/sys.a $(LDFLAGS)
+ 
+ #-----------LIBS
+@@ -93,10 +93,10 @@
+ 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)