diff --git a/configure b/configure
index bf2cf016d5..6b05f04aac 100755
--- a/configure
+++ b/configure
@@ -127,6 +127,7 @@ REBUILDOPT=''             # Can be set to --rebuild and passed to get_library.sh
 BUILDTESTOPT='silent'     # Set to blank to avoid asking about building libraries
 INSTALL_DAT='install_dat' # Target for installing data directory
 SPECIFIED_LIB_DIR=''      # Specified library directory
+LIBDIR='lib'              # Set by SetLibDir() to lib or lib64
 #CPPTRAJSRC=''             # CPPTRAJ source directory
 COMPERR='cpptrajcfg.compile.err'
 COMPOUT='cpptrajcfg.compile.out'
@@ -425,6 +426,17 @@ WrnMsg() {
   >&2 echo "Warning: $*"
 }
 
+#-------------------------------------------------------------------------------
+# SetLibDir <prefix> <lib>
+# Search for <prefix>/lib64/<lib> and set LIBDIR to lib64 if found.
+SetLibDir() {
+  LIBDIR='lib'
+  checklibfile="$1/lib64/$2"
+  if [ -f "$checklibfile" ] ; then
+    LIBDIR='lib64'
+  fi
+}
+
 #-------------------------------------------------------------------------------
 # Check for '--with' and '-no' library keys.
 CheckLibraryKeys() {
@@ -686,17 +698,19 @@ EOF
   nc_requires_hdf5_flags=0
   lhdf5_hl='-lhdf5_hl'
   lhdf5='-lhdf5'
+  SetLibDir "${LIB_HOME[$LHDF5]}" "libhdf5_hl.a"
   if [ ! -z "${LIB_HOME[$LHDF5]}" ] ; then
-    if [ -f "${LIB_HOME[$LHDF5]}/lib/libhdf5_hl.a" ] ; then
-      lhdf5_hl=${LIB_HOME[$LHDF5]}/lib/libhdf5_hl.a
+    if [ -f "${LIB_HOME[$LHDF5]}/$LIBDIR/libhdf5_hl.a" ] ; then
+      lhdf5_hl=${LIB_HOME[$LHDF5]}/$LIBDIR/libhdf5_hl.a
     fi
-    if [ -f "${LIB_HOME[$LHDF5]}/lib/libhdf5.a" ] ; then
-      lhdf5=${LIB_HOME[$LHDF5]}/lib/libhdf5.a
+    if [ -f "${LIB_HOME[$LHDF5]}/$LIBDIR/libhdf5.a" ] ; then
+      lhdf5=${LIB_HOME[$LHDF5]}/$LIBDIR/libhdf5.a
     fi
   fi
   if [ "${LIB_STAT[$LNETCDF]}" = 'specified' ] ; then
     export LD_LIBRARY_PATH="${LIB_HOME[$LNETCDF]}/lib:$LD_LIBRARY_PATH"
-    if [ ! -f "${LIB_HOME[$LNETCDF]}/lib/libnetcdf.so" -a -f "${LIB_HOME[$LNETCDF]}/lib/libnetcdf.a" ] ; then
+    SetLibDir "${LIB_HOME[$LNETCDF]}" "libnetcdf.a"
+    if [ ! -f "${LIB_HOME[$LNETCDF]}/$LIBDIR/libnetcdf.so" -a -f "${LIB_HOME[$LNETCDF]}/$LIBDIR/libnetcdf.a" ] ; then
       #echo "DEBUG: Only static NetCDF library is present."
       nc_requires_hdf5_flags=1
       hdf5_flags="$lhdf5_hl $lhdf5 -ldl ${LIB_FLAG[$LZIP]}"
@@ -738,9 +752,10 @@ EOF
   if [ $? -ne 0 ] ; then
     if [ "${LIB_STAT[$LHDF5]}" = 'enabled' ] ; then
       # See if there is already a version of HDF5 in CPPTRAJHOME
+      SetLibDir "$CPPTRAJHOME" "libhdf5_hl.a"
       LIB_STAT[$LHDF5]='specified'
       LIB_HOME[$LHDF5]=$CPPTRAJHOME
-      LIB_FLAG[$LHDF5]="$CPPTRAJHOME/lib/libhdf5_hl.a $CPPTRAJHOME/lib/${LIB_STTC[$LHDF5]} -ldl ${LIB_FLAG[$LZIP]}"
+      LIB_FLAG[$LHDF5]="$CPPTRAJHOME/$LIBDIR/libhdf5_hl.a $CPPTRAJHOME/$LIBDIR/${LIB_STTC[$LHDF5]} -ldl ${LIB_FLAG[$LZIP]}"
       LIB_INCL[$LHDF5]="-I$CPPTRAJHOME/include"
       TestProgram $BUILDTESTOPT "  Checking for bundled HDF5" "$CXX" "$CXXFLAGS ${LIB_INCL[$LHDF5]}" testp.cpp "${LIB_FLAG[$LHDF5]}"
       if [ $? -ne 0 ] ; then
@@ -784,11 +799,12 @@ EOF
     rebuild_netcdf='--rebuild'
   fi
   if [ $check_netcdf -ne 0 -o "${LIB_MAKE[$LNETCDF]}" == 'yes' ] ; then
+    SetLibDir "$CPPTRAJHOME" "${LIB_STTC[$LNETCDF]}"
     if [ "${LIB_STAT[$LNETCDF]}" = 'enabled' ] ; then
       # See if there is already a version of NetCDF in CPPTRAJHOME
       LIB_STAT[$LNETCDF]='specified'
       LIB_HOME[$LNETCDF]=$CPPTRAJHOME
-      LIB_FLAG[$LNETCDF]=$CPPTRAJHOME/lib/${LIB_STTC[$LNETCDF]}
+      LIB_FLAG[$LNETCDF]=$CPPTRAJHOME/$LIBDIR/${LIB_STTC[$LNETCDF]}
       LIB_INCL[$LNETCDF]="-I$CPPTRAJHOME/include"
       if [ "${LIB_STAT[$LHDF5]}" != 'off' ] ; then
         # Netcdf needs to know where hdf5 is
@@ -809,7 +825,7 @@ EOF
             echo "Overriding MAKE_COMMAND with 'make -j1' to avoid NetCDF4/HDF5 race conditions."
           fi
           PREFIX=$CPPTRAJHOME CC=$CC CFLAGS=$CFLAGS LIBNAME='netcdf' MAKE_COMMAND='make -j1' \
-              CPPFLAGS=${LIB_INCL[$LHDF5]} LDFLAGS="-L$CPPTRAJHOME/lib" \
+              CPPFLAGS=${LIB_INCL[$LHDF5]} LDFLAGS="-L$CPPTRAJHOME/$LIBDIR" \
               SRCDIR=$NETCDF_SRCDIR SRCTAR=$NETCDF_SRCTAR URL=$NETCDF_URL ./get_library.sh $rebuild_netcdf $NETCDF4_OPTS
           netcdferr=$?
         else