diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile snapfun_dir/Makefile
--- src/Makefile	2010-02-10 17:55:33.923514458 +0100
+++ snapfun_dir/Makefile	2010-02-23 10:38:31.391656287 +0100
@@ -1,6 +1,6 @@
 #=====================================================================
 F77			=	gfortran
-BIN			=	profnet_prof
+BIN			=	profnet_snapfun
 #=====================================================================
 ARCH			=	LINUX
 FFLAGS          	:= 	$(FFLAGS) -O2 -Wuninitialized
diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile.orig snapfun_dir/Makefile.orig
--- src/Makefile.orig	1970-01-01 01:00:00.000000000 +0100
+++ snapfun_dir/Makefile.orig	2010-02-23 10:38:31.395653152 +0100
@@ -0,0 +1,29 @@
+#=====================================================================
+F77			=	gfortran
+BIN			=	profnet_prof
+#=====================================================================
+ARCH			=	LINUX
+FFLAGS          	:= 	-O3 -fbounds-check -Wuninitialized
+FFLAGS          	:= 	$(FFLAGS) -Wall -Wno-unused
+#=====================================================================
+all:	$(BIN)
+
+#=====================================================================
+# Make Neural Network
+#=====================================================================
+
+NN_OBJS=prof.f lib-prof.f lib-sys-$(ARCH).f
+
+$(BIN): $(NN_OBJS)
+	@echo --- making $(BIN)
+	$(F77) -o $@ $(FFLAGS) $(NN_OBJS)
+
+clean:
+	rm -f *.o $(BIN)
+
+install:
+	mkdir -p $(DESTDIR)$(prefix)/bin && \
+		cp $(BIN) $(DESTDIR)$(prefix)/bin/
+
+.PHONY:	all clean install
+
diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f snapfun_dir/profPar.f
--- src/profPar.f	2010-02-23 10:17:25.315661972 +0100
+++ snapfun_dir/profPar.f	2010-02-23 10:38:31.399648899 +0100
@@ -32,20 +32,20 @@
 C lkajan: what it needs.
 C lkajan: The below numbers are the values used by prof as in
 C lkajan: prof{sec,acc}:
-      PARAMETER    (NUMIN_MAX=          800)
+      PARAMETER    (NUMIN_MAX=          900)
 C lkajan: The below number of 10000 is suitable for a method that
 C lkajan: presents a sample for each amino acids of a protein because
 C lkajan: we do not encounter a protein longer than 10000AA very often.
-      PARAMETER    (NUMSAM_MAX=       10000)
-      PARAMETER    (NUMHID_MAX=         100)
-      PARAMETER    (NUMOUT_MAX=          10)
-      PARAMETER    (NUMFILES_MAX=         2)
-      PARAMETER    (STPSWPMAX_MAX=        5)
+      PARAMETER    (NUMSAM_MAX=      100000)
+      PARAMETER    (NUMHID_MAX=          50)
+      PARAMETER    (NUMOUT_MAX=           2)
+      PARAMETER    (NUMFILES_MAX=       336)
+      PARAMETER    (STPSWPMAX_MAX=      400)
 C lkajan: STPMAX_MAX somehow controls the number of input vectors that can
 C lkajan: be evaluated in one go.  There is a simple integer array that gets
 C lkajan: allocated to STPMAX_MAX size.
-      PARAMETER    (STPMAX_MAX=           5)
-      PARAMETER    (NUMARG_MAX=         500)
+      PARAMETER    (STPMAX_MAX=      100000) 
+      PARAMETER    (NUMARG_MAX=         400)
 
 C                                G  M  T
 *----               -------------------------------------------------  *