diff --git a/src/ADIOS/Install.sh b/src/ADIOS/Install.sh
index bd0acb1414..0ee2c5428e 100644
--- a/src/ADIOS/Install.sh
+++ b/src/ADIOS/Install.sh
@@ -69,7 +69,7 @@ adios_SYSLIB=${ADIOS2_LIB}
     fi
 
     if (test -e ../Makefile.package.settings) then
-      sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings
+      sed -i -e '/^[ \t]*include.*ADIOS.*$/d' ../Makefile.package.settings
       # multiline form needed for BSD sed on Macs
       sed -i -e '4 i \
 include ../ADIOS/Makefile.lammps
@@ -85,7 +85,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*ADIOS.*$/d' ../Makefile.package.settings
   fi
 
   rm -f Makefile.lammps
diff --git a/src/ATC/Install.sh b/src/ATC/Install.sh
index e1dacdd7d6..2194685f92 100755
--- a/src/ATC/Install.sh
+++ b/src/ATC/Install.sh
@@ -60,7 +60,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*atc.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*atc.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/atc\/Makefile.lammps
@@ -74,7 +74,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*atc.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*atc.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/AWPMD/Install.sh b/src/AWPMD/Install.sh
index 70e87c3fbc..0e2e2d3473 100755
--- a/src/AWPMD/Install.sh
+++ b/src/AWPMD/Install.sh
@@ -46,7 +46,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*awpmd.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*awpmd.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/awpmd\/Makefile.lammps
@@ -60,7 +60,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*awpmd.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*awpmd.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/COLVARS/Install.sh b/src/COLVARS/Install.sh
index d67883a416..ebabfd7a1e 100755
--- a/src/COLVARS/Install.sh
+++ b/src/COLVARS/Install.sh
@@ -47,7 +47,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*colvars.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*colvars.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/colvars\/Makefile.lammps
@@ -62,7 +62,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*colvars.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*colvars.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/COMPRESS/Install.sh b/src/COMPRESS/Install.sh
index ab9dac33dc..c0d926cba4 100755
--- a/src/COMPRESS/Install.sh
+++ b/src/COMPRESS/Install.sh
@@ -44,7 +44,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*compress.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*compress.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/compress\/Makefile.lammps
@@ -58,7 +58,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*compress.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*compress.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/ELECTRODE/Install.sh b/src/ELECTRODE/Install.sh
index 65d0b404da..561df0dce0 100755
--- a/src/ELECTRODE/Install.sh
+++ b/src/ELECTRODE/Install.sh
@@ -49,11 +49,11 @@ if (test $1 = 1) then
         sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(electrode_SYSLIB) |' ../Makefile.package
     fi
     if (test -e ../Makefile.package.settings) then
-        sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings
+        sed -i -e '/^[ \t]*include.*electrode.*$/d' ../Makefile.package.settings
         # multiline form needed for BSD sed on Macs
         sed -i -e '4 i \
-            include ..\/..\/lib\/electrode\/Makefile.lammps
-                    ' ../Makefile.package.settings
+include ..\/..\/lib\/electrode\/Makefile.lammps
+' ../Makefile.package.settings
     fi
 
 elif (test $1 = 0) then
@@ -61,7 +61,7 @@ elif (test $1 = 0) then
         sed -i -e 's/[^ \t]*electrode[^ \t]* //g' ../Makefile.package
     fi
     if (test -e ../Makefile.package.settings) then
-        sed -i -e '/^include.*electrode.*$/d' ../Makefile.package.settings
+        sed -i -e '/^[ \t]*include.*electrode.*$/d' ../Makefile.package.settings
     fi
 fi
 
diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh
index 1768ec024f..d28e6260f8 100755
--- a/src/GPU/Install.sh
+++ b/src/GPU/Install.sh
@@ -176,7 +176,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*gpu.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/gpu\/Makefile.lammps
@@ -191,7 +191,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*gpu.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/H5MD/Install.sh b/src/H5MD/Install.sh
index 1070afaa96..ee442d80bc 100755
--- a/src/H5MD/Install.sh
+++ b/src/H5MD/Install.sh
@@ -45,7 +45,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*h5md.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*h5md.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/h5md\/Makefile.lammps
@@ -60,7 +60,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*h5md.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*h5md.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/KIM/Install.sh b/src/KIM/Install.sh
index 7ddb9c8227..533f4f997a 100755
--- a/src/KIM/Install.sh
+++ b/src/KIM/Install.sh
@@ -44,7 +44,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*kim.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/kim\/Makefile.lammps
@@ -58,7 +58,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*kim.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
index 063ea44720..5c46a89e26 100755
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@@ -374,7 +374,7 @@ if (test $1 = 1) then
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/CXX\ =\ \$(CC)/d' ../Makefile.package.settings
-    sed -i -e '/^include.*kokkos.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*kokkos.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 CXX = $(CC)
@@ -401,7 +401,7 @@ elif (test $1 = 0) then
 
   if (test -e ../Makefile.package.settings) then
     sed -i -e '/CXX\ =\ \$(CC)/d' ../Makefile.package.settings
-    sed -i -e '/^include.*kokkos.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*kokkos.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/LATTE/Install.sh b/src/LATTE/Install.sh
index 73f8bc24cb..4d895ca434 100755
--- a/src/LATTE/Install.sh
+++ b/src/LATTE/Install.sh
@@ -47,7 +47,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*latte.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*latte.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/latte\/Makefile.lammps
@@ -61,7 +61,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*latte.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*latte.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/MACHDYN/Install.sh b/src/MACHDYN/Install.sh
index bf18c332f3..604f53f8b1 100755
--- a/src/MACHDYN/Install.sh
+++ b/src/MACHDYN/Install.sh
@@ -45,7 +45,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*machdyn.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/machdyn\/Makefile.lammps
@@ -59,7 +59,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*machdyn.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*machdyn.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/MDI/Install.sh b/src/MDI/Install.sh
index bc19162a17..804e66be5e 100755
--- a/src/MDI/Install.sh
+++ b/src/MDI/Install.sh
@@ -49,7 +49,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*mdi.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/mdi\/Makefile.lammps
@@ -65,7 +65,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*mdi.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/MESONT/Install.sh b/src/MESONT/Install.sh
index 6e51bfae64..09e6c03dde 100644
--- a/src/MESONT/Install.sh
+++ b/src/MESONT/Install.sh
@@ -47,7 +47,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*mesont.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*mesont.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/mesont\/Makefile.lammps
@@ -61,7 +61,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*mesont.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*mesont.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/ML-HDNNP/Install.sh b/src/ML-HDNNP/Install.sh
index 74e5f1b91e..f343f38851 100644
--- a/src/ML-HDNNP/Install.sh
+++ b/src/ML-HDNNP/Install.sh
@@ -46,7 +46,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*hdnnp.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/hdnnp\/Makefile.lammps
@@ -60,7 +60,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*hdnnp.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*hdnnp.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/ML-IAP/Install.sh b/src/ML-IAP/Install.sh
index 27c9b19b01..18812c6026 100755
--- a/src/ML-IAP/Install.sh
+++ b/src/ML-IAP/Install.sh
@@ -52,7 +52,7 @@ if (test $1 = 1) then
       sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package
     fi
     if (test -e ../Makefile.package.settings) then
-      sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
+      sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings
       # multiline form needed for BSD sed on Macs
       sed -i -e '4 i \
 include ..\/..\/lib\/python\/Makefile.mliap_python
@@ -68,7 +68,7 @@ elif (test $1 = 0) then
   fi
   rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h \
     ../mliap_unified_couple.cpp ../mliap_unified_couple.h
-  sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
+  sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings
 
 elif (test $1 = 2) then
   if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then
@@ -77,12 +77,12 @@ elif (test $1 = 2) then
     fi
     rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h \
       ../mliap_unified_couple.cpp ../mliap_unified_couple.h
-    sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings
     if (test -e ../Makefile.package) then
       sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package
     fi
     if (test -e ../Makefile.package.settings) then
-      sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
+      sed -i -e '/^[ \t]*include.*python.*mliap_python.*$/d' ../Makefile.package.settings
       # multiline form needed for BSD sed on Macs
       sed -i -e '4 i \
 include ..\/..\/lib\/python\/Makefile.mliap_python
diff --git a/src/ML-PACE/Install.sh b/src/ML-PACE/Install.sh
index c099ddd2c4..c0a0958424 100644
--- a/src/ML-PACE/Install.sh
+++ b/src/ML-PACE/Install.sh
@@ -44,7 +44,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*pace.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/pace\/Makefile.lammps
@@ -58,7 +58,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*pace.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/ML-QUIP/Install.sh b/src/ML-QUIP/Install.sh
index 20174e664a..03f93c14b8 100755
--- a/src/ML-QUIP/Install.sh
+++ b/src/ML-QUIP/Install.sh
@@ -44,7 +44,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*quip.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*quip.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/quip\/Makefile.lammps\
@@ -58,7 +58,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*quip.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*quip.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/MOLFILE/Install.sh b/src/MOLFILE/Install.sh
index 85885f66b9..3ae4357ade 100755
--- a/src/MOLFILE/Install.sh
+++ b/src/MOLFILE/Install.sh
@@ -44,7 +44,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*molfile.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*molfile.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/molfile\/Makefile.lammps
@@ -58,7 +58,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*molfile.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*molfile.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/MSCG/Install.sh b/src/MSCG/Install.sh
index 353403c7da..67f0f837ce 100755
--- a/src/MSCG/Install.sh
+++ b/src/MSCG/Install.sh
@@ -43,7 +43,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*mscg.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*mscg.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/mscg\/Makefile.lammps
@@ -57,7 +57,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*mscg.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*mscg.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/Makefile b/src/Makefile
index 923cc535fd..39937c58d6 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -55,7 +55,7 @@ PACKAGE = \
 	awpmd \
 	bocs \
 	body \
-        bpm \
+	bpm \
 	brownian \
 	cg-dna \
 	cg-spica \
diff --git a/src/NETCDF/Install.sh b/src/NETCDF/Install.sh
index 4d21f0f894..8c70d84fd8 100755
--- a/src/NETCDF/Install.sh
+++ b/src/NETCDF/Install.sh
@@ -42,7 +42,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*netcdf.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/netcdf\/Makefile.lammps
@@ -57,7 +57,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*netcdf.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/PLUGIN/Install.sh b/src/PLUGIN/Install.sh
index 0df642193e..86de36d7df 100755
--- a/src/PLUGIN/Install.sh
+++ b/src/PLUGIN/Install.sh
@@ -44,7 +44,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*plugin.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/plugin\/Makefile.lammps
@@ -58,7 +58,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*plugin.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*plugin.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/PLUMED/Install.sh b/src/PLUMED/Install.sh
index f879d42feb..500a55ec77 100755
--- a/src/PLUMED/Install.sh
+++ b/src/PLUMED/Install.sh
@@ -45,7 +45,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*plumed.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*plumed.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/plumed\/Makefile.lammps
@@ -59,7 +59,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*plumed.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*plumed.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/POEMS/Install.sh b/src/POEMS/Install.sh
index be407d76f0..37f8404738 100755
--- a/src/POEMS/Install.sh
+++ b/src/POEMS/Install.sh
@@ -44,7 +44,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*poems.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*poems.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/poems\/Makefile.lammps
@@ -58,7 +58,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*poems.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*poems.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/PYTHON/Install.sh b/src/PYTHON/Install.sh
index 8c394d43ad..b23cf574f8 100755
--- a/src/PYTHON/Install.sh
+++ b/src/PYTHON/Install.sh
@@ -50,7 +50,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*python.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*python.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/python\/Makefile.lammps
@@ -65,7 +65,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*python.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*python.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/QMMM/Install.sh b/src/QMMM/Install.sh
index 4bede66d80..0c9643b84e 100755
--- a/src/QMMM/Install.sh
+++ b/src/QMMM/Install.sh
@@ -47,7 +47,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*qmmm.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*qmmm.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/qmmm\/Makefile.lammps
@@ -62,7 +62,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*qmmm.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*qmmm.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/VORONOI/Install.sh b/src/VORONOI/Install.sh
index 6373506b19..c7f897e5e6 100755
--- a/src/VORONOI/Install.sh
+++ b/src/VORONOI/Install.sh
@@ -48,7 +48,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*voronoi.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*voronoi.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/voronoi\/Makefile.lammps
@@ -63,7 +63,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*voronoi.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*voronoi.*$/d' ../Makefile.package.settings
   fi
 
 fi
diff --git a/src/VTK/Install.sh b/src/VTK/Install.sh
index 3749242fb2..fda4287d51 100755
--- a/src/VTK/Install.sh
+++ b/src/VTK/Install.sh
@@ -43,7 +43,7 @@ if (test $1 = 1) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*vtk.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*vtk.*$/d' ../Makefile.package.settings
     # multiline form needed for BSD sed on Macs
     sed -i -e '4 i \
 include ..\/..\/lib\/vtk\/Makefile.lammps
@@ -58,7 +58,7 @@ elif (test $1 = 0) then
   fi
 
   if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*vtk.*$/d' ../Makefile.package.settings
+    sed -i -e '/^[ \t]*include.*vtk.*$/d' ../Makefile.package.settings
   fi
 
 fi