diff --git a/patches/gromacs-4.5.5.config b/patches/gromacs-4.5.5.config
index 962025998ce09bfb4cba64d75d17c5127cb95f42..8529732bb2d56c68645d017d87ec94464e22f7e3 100644
--- a/patches/gromacs-4.5.5.config
+++ b/patches/gromacs-4.5.5.config
@@ -21,7 +21,7 @@ function plumed_after_revert(){
 function plumed_patch_info(){
   echo ""
   echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
-  echo "Patching must be done _after_ gromacs has been configured, _before_ gromacs is compiled"
+  echo "Patching must be done _after_ gromacs has been configured but  _before_ gromacs is compiled"
   echo 
   echo "For more information on gromacs you should visit http://www.gromacs.org"
 }
diff --git a/patches/gromacs-4.6.3.config b/patches/gromacs-4.6.3.config
index 36840c3ba11a78132bc5a2e7dc6b7040a88df551..b5d89332bfd90c7da73c33769c3f5ff3e8529642 100644
--- a/patches/gromacs-4.6.3.config
+++ b/patches/gromacs-4.6.3.config
@@ -8,7 +8,7 @@ function plumed_preliminary_test(){
 function plumed_patch_info(){
   echo ""
   echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
-  echo "Patching must be done _before_ cmake command is invoked"
+  echo "Patching must be done _before_ the cmake command is invoked"
   echo
   echo "For more information on gromacs you should visit http://www.gromacs.org"
 }
diff --git a/patches/lammps-6Apr13.config b/patches/lammps-6Apr13.config
index abdd1437c429a6af1039df54721bd86298477fb2..a83ff65c1a8e63d7f15d7d5aae0e6bdcafcc0f35 100644
--- a/patches/lammps-6Apr13.config
+++ b/patches/lammps-6Apr13.config
@@ -18,9 +18,9 @@ function plumed_patch_info(){
   echo ""
   echo "PLUMED can be incorporated into LAMMPS using a simple patching procedure."
   echo "Patching must be done _before_ LAMMPS is configured."
-  echo "After patching, one should also enable PLUMED with"
+  echo "After patching, one should enable PLUMED using the command"
   echo "make yes-user-plumed"
-  echo "In the same way, before reverting one should disable PLUMED with"
+  echo "In the same way, before reverting one should disable PLUMED using the command"
   echo "make no-user-plumed"
   echo 
   echo "For more information on LAMMPS you should visit http://lammps.sandia.gov/"
diff --git a/user-doc/extract b/user-doc/extract
index 4260ea4ae15a4b538b114ac2a67fa6a978ba229e..d361a36779f675d14d53204cdbd247ffd939b5d9 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -142,8 +142,8 @@ do
         
         # Find src files in module and add a link to the module description
         for srcfile in `ls ../src/"$file"/*cpp` ; do
-            ndocs=`grep PLUMEDOC "$srcfile" | wc -l | awk '{print $1}'`
-            for ((line=1;line<$ndocs;++line)) ; do
+            ndocs=`grep PLUMEDOC "$srcfile" | grep -v END | wc -l | awk '{print $1}'`
+            for ((line=1;line<=$ndocs;++line)) ; do
                docfile=`grep PLUMEDOC "$srcfile" | grep -v END | head -n $line | tail -n 1 | awk '{print $3}'`
                cat automatic/"$docfile".tmp |
                {