Index: head/science/namd/Makefile
===================================================================
--- head/science/namd/Makefile	(revision 479267)
+++ head/science/namd/Makefile	(revision 479268)
@@ -1,81 +1,78 @@
 # $FreeBSD$
 
 PORTNAME=	namd
-DISTVERSION=	2-12-211
-DISTVERSIONSUFFIX=	-gfdf7ea56
+DISTVERSION=	2.12
 CATEGORIES=	science
+DISTNAME=	${PORTNAME:tu}_${DISTVERSION}_Source
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Computer software for molecular dynamics simulation
 
 LICENSE=	NAMD_MOLECULAR_DYNAMICS_LICENSE
 LICENSE_NAME=	NAMD Molecular Dynamics Software
 LICENSE_FILE=	${WRKSRC}/license.txt
 LICENSE_PERMS=	no-auto-accept no-dist-mirror no-pkg-mirror # No redistribution is allowed.
 
 ONLY_FOR_ARCHS=	amd64 i386
 ONLY_FOR_ARCHS_REASON=	Not clear if it can be built on other architectures
 BROKEN_i386=	need to fix the fft library handling
 
-FETCH_DEPENDS=	git:devel/git
 BUILD_DEPENDS=	bash:shells/bash \
 		${LOCALBASE}/include/fftw3.h:math/fftw3
 LIB_DEPENDS=	libck.so:net/charm \
 		libfftw3f.so:math/fftw3-float
 
 USES=		fortran gmake localbase:ldflags python:build shebangfix tcl
 SHEBANG_FILES=	config
 
 GIT_URL=	https://charm.cs.illinois.edu/gerrit/namd.git
 
 ARCH_STR=	Linux-${ARCH:S/amd64/x86_64/:S/i386/x86/}-g++
 ARCH_STR_CHARM=	linux${ARCH:S/amd64/64/:S/i386/32/}
 
 PATCH_WRKSRC=	${WRKSRC}
 BUILD_WRKSRC=	${WRKSRC}/${ARCH_STR}
 
 CFLAGS+=	-D_NO_MALLOC_H -D_NO_ALLOCA_H
 CXXFLAGS+=	-D_NO_MALLOC_H -D_NO_ALLOCA_H
 
 BINARY_ALIAS=	gcc=${CC} g++=${CXX}
 
 PLIST_FILES=	bin/flipbinpdb \
 		bin/flipdcd \
 		bin/namd2 \
 		bin/psfgen \
 		bin/sortreplicas
 
 local-makesum: # Workaround: the generic 'make makesum' is broken when custom do-fetch is defined: it calls ${SCRIPTSDIR}/do-fetch.sh.
 	@${MAKE} distclean fetch makesum
 
 do-fetch:
-	@if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \
-	  ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \
-	  cd ${DISTDIR}/${DIST_SUBDIR} && \
-	    git clone -q ${GIT_URL} ${PORTNAME}-${DISTVERSIONFULL} && \
-	    (cd ${PORTNAME}-${DISTVERSIONFULL} && git reset -q --hard ${DISTVERSIONFULL} && ${RM} -r .git) && \
-	    ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \
-	    ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=C ${SORT} -z | \
-	        ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} --format=bsdtar --uid 0 --gid 0 --options gzip:!timestamp --no-recursion --null -T - && \
-	    ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \
+	@if ! [ -f "${DISTDIR}/${DISTFILES}" ]; then \
+	  ${ECHO} "(!!)"; \
+	  ${ECHO} "(!!) Please download the release tarball of the version ${DISTVERSION} (${DISTFILES})"; \
+	  ${ECHO} "(!!) from https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD,"; \
+	  ${ECHO} "(!!) put it into ${DISTDIR}, and run 'make' again."; \
+	  ${ECHO} "(!!)"; \
+	  ${FALSE}; \
 	fi
 
 do-configure:
 	@cd ${WRKSRC} && ${ECHO} "CHARMBASE=${LOCALBASE}" > Make.config
 	@cd ${WRKSRC} && ./config ${ARCH_STR} --charm-arch multicore-${ARCH_STR_CHARM} ${ARCH:S/amd64/--with-fftw3/:S/${ARCH}//}
 	@${REINPLACE_CMD} 's|CHARMBASE = .*|CHARMBASE = ${LOCALBASE}|' ${WRKSRC}/Make.charm
 	@${REINPLACE_CMD} '\
 		s|FFTDIR=.*|FFTDIR=${LOCALBASE}|; \
 		s|-lsfftw|-lfft3f|; \
 		s|-lsrfftw|-lrfft3f|; \
 		s|TCLDIR=.*|TCLDIR=${LOCALBASE}/include/tcl8.6|; \
 		s|TCLINCL=.*|TCLINCL=-I${LOCALBASE}/include/tcl8.6|; \
 		s|TCLLIB=.*|TCLLIB=-L${LOCALBASE}/lib -ltcl86 -lpthread|' \
 		${WRKSRC}/arch/Linux*
 
 do-install:
 .for e in namd2 flipbinpdb flipdcd psfgen sortreplicas
 	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin
 .endfor
 
 .include <bsd.port.mk>
Index: head/science/namd/distinfo
===================================================================
--- head/science/namd/distinfo	(revision 479267)
+++ head/science/namd/distinfo	(revision 479268)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1536445358
-SHA256 (namd-2-12-211-gfdf7ea56.tar.gz) = 2ab3a98f7cc9fa997088502aa87ad8cfe9218b35d4b783b7370a5d5d49f7fe15
-SIZE (namd-2-12-211-gfdf7ea56.tar.gz) = 8278948
+TIMESTAMP = 1536472466
+SHA256 (NAMD_2.12_Source.tar.gz) = 436d11e4ff78136c7463d448d2eee92509a39b4c03cab8d07176bb20ddcb675a
+SIZE (NAMD_2.12_Source.tar.gz) = 9706667
Index: head/science/namd/files/patch-Makefile
===================================================================
--- head/science/namd/files/patch-Makefile	(revision 479267)
+++ head/science/namd/files/patch-Makefile	(revision 479268)
@@ -1,11 +1,11 @@
---- Makefile.orig	1970-01-01 00:00:00 UTC
+--- Makefile.orig	2018-09-09 05:56:50 UTC
 +++ Makefile
-@@ -435,7 +435,7 @@ LIBS = $(CUDAOBJS) $(PLUGINLIB) $(SBLIB)
+@@ -436,7 +436,7 @@ LIBS = $(CUDAOBJS) $(PLUGINLIB) $(SBLIB)
  
  # CXX is platform dependent
- CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTI)$(COLVARSINCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP)
+ CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP)
 -CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS)
 +CXXFLAGS += $(CXXBASEFLAGS) $(CXXOPTS)
  CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
  CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
  CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
Index: head/science/namd/files/patch-config
===================================================================
--- head/science/namd/files/patch-config	(revision 479267)
+++ head/science/namd/files/patch-config	(revision 479268)
@@ -1,11 +1,11 @@
---- config.orig	2018-09-07 20:23:43 UTC
+--- config.orig	2018-09-09 05:55:48 UTC
 +++ config
-@@ -582,7 +582,7 @@ function error_exists {
-   if [ -n "$CHARM_OPTS" ]; then
+@@ -535,7 +535,7 @@ begin:
+   if ( $?CHARM_OPTS ) then
      echo "CHARMOPTS = $CHARM_OPTS" >> Make.config
-   fi
+   endif
 -  echo 'CHARM = $(CHARMBASE)/$(CHARMARCH)' >> Make.config
 +  echo 'CHARM = $(CHARMBASE)' >> Make.config
-   ARCH_SUFFIX=""
-   [[ "$CHARM_ARCH" == *-scyld* ]] && ARCH_SUFFIX=${ARCH_SUFFIX}-Scyld
-   if [[ "$CHARM_ARCH" == *-clustermatic* ]]; then
+   set ARCH_SUFFIX = ""
+   if ( $CHARM_ARCH =~ *-scyld* ) set ARCH_SUFFIX = ${ARCH_SUFFIX}-Scyld
+   if ( $CHARM_ARCH =~ *-clustermatic* ) then