gentoo-overlay/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch

diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile
index d2c2d3b..d1f02e5 100644
--- a/build/linux/debug/Makefile
+++ b/build/linux/debug/Makefile
@@ -1,6 +1,6 @@
 BASE=/usr/local
 BOOST_VERSION=1_41
-C_PLATFORM=-static-libgcc -pthread
+C_PLATFORM=-pthread
 GPP=/usr/bin/g++
 C_OPTIONS= -g
 BOOST_LIB_VERSION=
diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile
index bfbcc1e..c9fd630 100644
--- a/build/linux/release/Makefile
+++ b/build/linux/release/Makefile
@@ -1,6 +1,6 @@
 BASE=/usr/local
 BOOST_VERSION=1_41
-C_PLATFORM=-static-libgcc -pthread
+C_PLATFORM=-pthread
 GPP=/usr/bin/g++
 C_OPTIONS= -O3 -DNDEBUG
 BOOST_LIB_VERSION=
diff --git a/build/makefile_common b/build/makefile_common
index 885935c..e72142d 100644
--- a/build/makefile_common
+++ b/build/makefile_common
@@ -1,30 +1,30 @@
-BOOST_INCLUDE = $(BASE)/include/boost-${BOOST_VERSION}
+BOOST_INCLUDE = $(BASE)/include/boost
 
 LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o
 MAINOBJ = main.o
 SPLITOBJ = split.o
 
-INCFLAGS = -I $(BOOST_INCLUDE)
+INCFLAGS = -I$(BOOST_INCLUDE)
 
-CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+CC = ${GPP} ${C_PLATFORM} ${C_OPTIONS} $(INCFLAGS)
 
-LDFLAGS = -L$(BASE)/lib -L.
+LDFLAGS += -L.
 
-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
+LIBS = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread
 
 .SUFFIXES: .cpp .o
 
 %.o : ../../../src/lib/%.cpp 
-	$(CC) $(CFLAGS) -o $@ -c $< 
+	$(CC) $(CXXFLAGS) -o $@ -c $< 
 
 %.o : ../../../src/design/%.cpp 
-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
+	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
 	
 %.o : ../../../src/main/%.cpp 
-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
+	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
 
 %.o : ../../../src/split/%.cpp 
-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
+	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
 
 all: vina vina_split