--- /dev/null
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.1 2011/07/28 13:19:06 alexxy Exp $
+
+EAPI=4
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+ AmberTools-${PV}.tar.bz2
+ mirror://gentoo/${P}-bugfix_1-10.patch.xz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+ virtual/cblas
+ virtual/lapack
+ sci-libs/clapack
+ sci-libs/arpack
+ sci-libs/cifparse-obj
+ sci-chemistry/mopac7
+ sci-libs/netcdf
+ sci-libs/fftw:2.1
+ sci-chemistry/reduce
+ virtual/fortran"
+DEPEND="${RDEPEND}
+ dev-util/byacc
+ dev-libs/libf2c
+ sys-devel/ucpp"
+S="${WORKDIR}/amber11"
+
+pkg_nofetch() {
+ einfo "Go to ${HOMEPAGE} and get ${A}"
+ einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ if use openmp; then
+ tc-has-openmp || \
+ die "Please select an openmp capable compiler like gcc[openmp]"
+ fi
+ AMBERHOME="${S}"
+}
+
+src_prepare() {
+ epatch \
+ "${WORKDIR}/${P}-bugfix_1-10.patch" \
+ "${FILESDIR}/${P}-gentoo.patch"
+ cd AmberTools/src
+ 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:-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=$(tc-getFC):g" \
+ -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+ -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+ -e "s:-O3::g" \
+ -i configure || die
+ sed -e "s:arsecond_:arscnd_:g" \
+ -i sff/time.c \
+ -i sff/sff.h \
+ -i sff/sff.c || die
+ sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
+ -i nss/Makefile || die
+
+ local myconf
+
+ use X || myconf="${myconf} -noX11"
+
+ for x in mpi openmp; do
+ use ${x} && myconf="${myconf} -${x}"
+ done
+
+ ./configure \
+ ${myconf} \
+ -nobintraj \
+ -nomdgx \
+ -nopython \
+ -nomtkpp \
+ gnu
+# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+}
+
+src_compile() {
+ cd AmberTools/src
+ emake || die
+}
+
+src_install() {
+ rm -r bin/chemistry bin/MMPBSA_mods
+ rm bin/ante-MMPBSA.py bin/extractFrcmod.py
+ for x in bin/*
+ do dobin ${x} || die
+ done
+ rm "${ED}/usr/bin/yacc"
+ dobin AmberTools/src/antechamber/mopac.sh
+ sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+ -i "${ED}/usr/bin/mopac.sh" || die
+ # Make symlinks untill binpath for amber will be fixed
+ dodir /usr/share/${PN}/bin
+ cd "${ED}/usr/bin"
+ for x in *
+ do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+ done
+ cd "${S}"
+# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
+# -i "${ED}/usr/bin/xleap" \
+# -i "${ED}/usr/bin/tleap" || die
+ dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+ dolib.a lib/*
+ insinto /usr/include/${PN}
+ doins include/*
+ insinto /usr/share/${PN}
+ doins -r dat
+ cd AmberTools
+ doins -r benchmarks
+ doins -r examples
+ doins -r test
+ cat >> "${T}"/99ambertools <<- EOF
+ AMBERHOME="${EPREFIX}/usr/share/ambertools"
+ EOF
+ doenvd "${T}"/99ambertools
+}
--- /dev/null
+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)
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