From: Teemu Murtola <teemu.murtola@gmail.com>
Date: Mon, 2 Jun 2014 18:36:21 +0000 (+0300)
Subject: Move index.* to topology/
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=ffc891f7dc35856bf8575cdc6ef62e09f8bd2473;p=alexxy%2Fgromacs.git

Move index.* to topology/

- Move index.h and index.c to topology/.
- Remove some unused and duplicate includes.
- Convert the source file to C++ (scanf issues suppressed for now).

Change-Id: I99374f5d2e53b6c26bf6441b630234177c83affb
---

diff --git a/src/contrib/do_multiprot.c b/src/contrib/do_multiprot.c
index f5647c5aad..d7943a2659 100644
--- a/src/contrib/do_multiprot.c
+++ b/src/contrib/do_multiprot.c
@@ -47,7 +47,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/xvgr.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gstat.h"
 #include "gromacs/fileio/tpxio.h"
 #include "viewit.h"
diff --git a/src/contrib/do_shift.c b/src/contrib/do_shift.c
index c66a810c9d..fd20a5ada9 100644
--- a/src/contrib/do_shift.c
+++ b/src/contrib/do_shift.c
@@ -48,7 +48,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gstat.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/pdbio.h"
 
 void cat(FILE *out,char *fn,real t)
diff --git a/src/contrib/g_anavel.c b/src/contrib/g_anavel.c
index 6cb062fe49..96da5c85bb 100644
--- a/src/contrib/g_anavel.c
+++ b/src/contrib/g_anavel.c
@@ -46,7 +46,6 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
 #include "copyrite.h"
-#include "index.h"
 #include "gromacs/fileio/tpxio.h"
 
 int main(int argc,char *argv[])
diff --git a/src/contrib/gmx_sdf.c b/src/contrib/gmx_sdf.c
index 39cb0f5545..9e003626bd 100644
--- a/src/contrib/gmx_sdf.c
+++ b/src/contrib/gmx_sdf.c
@@ -29,7 +29,7 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
 #include "gstat.h"
diff --git a/src/contrib/hexamer.c b/src/contrib/hexamer.c
index 22117c73a9..bd477eb91b 100644
--- a/src/contrib/hexamer.c
+++ b/src/contrib/hexamer.c
@@ -46,7 +46,6 @@
 #include "macros.h"
 #include "copyrite.h"
 #include "gromacs/commandline/pargs.h"
-#include "index.h"
 #include "gromacs/math/vec.h"
 #include "typedefs.h"
 #include "gbutil.h"
diff --git a/src/gromacs/fileio/pdbio.c b/src/gromacs/fileio/pdbio.c
index a4c1487d68..ecbfa7c75b 100644
--- a/src/gromacs/fileio/pdbio.c
+++ b/src/gromacs/fileio/pdbio.c
@@ -45,7 +45,6 @@
 #include <string.h>
 
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/index.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/utility/futil.h"
@@ -55,6 +54,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/cstringutil.h"
diff --git a/src/gromacs/gmxana/dlist.c b/src/gromacs/gmxana/dlist.c
index 3f86100cbe..f44fe45ec8 100644
--- a/src/gromacs/gmxana/dlist.c
+++ b/src/gromacs/gmxana/dlist.c
@@ -44,7 +44,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gstat.h"
 #include "gromacs/utility/fatalerror.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 
 t_dlist *mk_dlist(FILE *log,
                   t_atoms *atoms, int *nlist,
diff --git a/src/gromacs/gmxana/expfit.c b/src/gromacs/gmxana/expfit.c
index ee125c8b8e..d0731c210a 100644
--- a/src/gromacs/gmxana/expfit.c
+++ b/src/gromacs/gmxana/expfit.c
@@ -47,7 +47,6 @@
 #include "gromacs/utility/futil.h"
 #include "gstat.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
 
 #include "gromacs/utility/fatalerror.h"
 
diff --git a/src/gromacs/gmxana/gmx_anaeig.c b/src/gromacs/gmxana/gmx_anaeig.c
index e0b4d1efe7..2c46a8f7ef 100644
--- a/src/gromacs/gmxana/gmx_anaeig.c
+++ b/src/gromacs/gmxana/gmx_anaeig.c
@@ -49,7 +49,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/tpxio.h"
diff --git a/src/gromacs/gmxana/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c
index 2795b3d2f7..b5c3d7e1a3 100644
--- a/src/gromacs/gmxana/gmx_angle.c
+++ b/src/gromacs/gmxana/gmx_angle.c
@@ -47,7 +47,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "macros.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/xvgr.h"
diff --git a/src/gromacs/gmxana/gmx_bundle.c b/src/gromacs/gmxana/gmx_bundle.c
index 7947559761..c0ffc08d9a 100644
--- a/src/gromacs/gmxana/gmx_bundle.c
+++ b/src/gromacs/gmxana/gmx_bundle.c
@@ -46,7 +46,7 @@
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/tpxio.h"
diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index 5cb3c68f89..89882e96e9 100644
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -50,7 +50,7 @@
 #include "macros.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/units.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
index 3d49a95dea..765105707b 100644
--- a/src/gromacs/gmxana/gmx_cluster.c
+++ b/src/gromacs/gmxana/gmx_cluster.c
@@ -51,7 +51,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/math/vec.h"
 #include "macros.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/random/random.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
diff --git a/src/gromacs/gmxana/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
index b3f770b86c..0ebf0826ea 100644
--- a/src/gromacs/gmxana/gmx_clustsize.c
+++ b/src/gromacs/gmxana/gmx_clustsize.c
@@ -49,7 +49,7 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
 #include "gromacs/math/units.h"
diff --git a/src/gromacs/gmxana/gmx_confrms.c b/src/gromacs/gmxana/gmx_confrms.c
index 1ffdeee686..da05a0157d 100644
--- a/src/gromacs/gmxana/gmx_confrms.c
+++ b/src/gromacs/gmxana/gmx_confrms.c
@@ -48,7 +48,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/fileio/confio.h"
diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
index bc77018c30..5b8c50f6c7 100644
--- a/src/gromacs/gmxana/gmx_covar.c
+++ b/src/gromacs/gmxana/gmx_covar.c
@@ -52,7 +52,7 @@
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/xvgr.h"
diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index 39b9b1b706..5167a590c2 100644
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -49,7 +49,7 @@
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/math/units.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/statistics/statistics.h"
 #include "gmx_ana.h"
 #include "macros.h"
diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index 768d0f9082..1cbd6e8ce7 100644
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -49,7 +49,7 @@
 #include "gstat.h"
 #include "viewit.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/math/units.h"
diff --git a/src/gromacs/gmxana/gmx_densmap.c b/src/gromacs/gmxana/gmx_densmap.c
index e3205c6ce9..c17f540010 100644
--- a/src/gromacs/gmxana/gmx_densmap.c
+++ b/src/gromacs/gmxana/gmx_densmap.c
@@ -48,7 +48,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "txtdump.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/gmx_densorder.cpp b/src/gromacs/gmxana/gmx_densorder.cpp
index 67acd98ed2..020c746947 100644
--- a/src/gromacs/gmxana/gmx_densorder.cpp
+++ b/src/gromacs/gmxana/gmx_densorder.cpp
@@ -46,7 +46,7 @@
 #include "gstat.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/math/units.h"
diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index 9e740d6c3b..2a0ef2cc07 100644
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -50,7 +50,7 @@
 #include "txtdump.h"
 #include "gromacs/statistics/statistics.h"
 #include "gstat.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/random/random.h"
 #include "names.h"
 #include "gromacs/math/units.h"
diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index 1efdfb4170..046c51cf12 100644
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -53,7 +53,7 @@
 #include "gstat.h"
 #include "main.h"
 #include "gromacs/fileio/pdbio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "mdatoms.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/gmx_do_dssp.c b/src/gromacs/gmxana/gmx_do_dssp.c
index 7b0cd14213..346bfa03e6 100644
--- a/src/gromacs/gmxana/gmx_do_dssp.c
+++ b/src/gromacs/gmxana/gmx_do_dssp.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "macros.h"
 #include "gromacs/fileio/pdbio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gstat.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index 104e42260d..c695cbe1fb 100644
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -49,7 +49,6 @@
 #include "macros.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/units.h"
-#include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "txtdump.h"
diff --git a/src/gromacs/gmxana/gmx_dyecoupl.c b/src/gromacs/gmxana/gmx_dyecoupl.c
index cc492abd05..55db291afa 100644
--- a/src/gromacs/gmxana/gmx_dyecoupl.c
+++ b/src/gromacs/gmxana/gmx_dyecoupl.c
@@ -42,7 +42,7 @@
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
diff --git a/src/gromacs/gmxana/gmx_dyndom.c b/src/gromacs/gmxana/gmx_dyndom.c
index 9106fa66f4..27a157d521 100644
--- a/src/gromacs/gmxana/gmx_dyndom.c
+++ b/src/gromacs/gmxana/gmx_dyndom.c
@@ -38,7 +38,7 @@
 #include <config.h>
 #endif
 
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/math/units.h"
 #include "gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_editconf.c b/src/gromacs/gmxana/gmx_editconf.c
index 3bf14dbf76..1c1d18c702 100644
--- a/src/gromacs/gmxana/gmx_editconf.c
+++ b/src/gromacs/gmxana/gmx_editconf.c
@@ -45,7 +45,7 @@
 #include "gromacs/fileio/confio.h"
 #include "macros.h"
 #include "gromacs/fileio/strdb.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "typedefs.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
 #include "gromacs/math/units.h"
diff --git a/src/gromacs/gmxana/gmx_filter.c b/src/gromacs/gmxana/gmx_filter.c
index 51b2fad0d1..e51ceff061 100644
--- a/src/gromacs/gmxana/gmx_filter.c
+++ b/src/gromacs/gmxana/gmx_filter.c
@@ -45,7 +45,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "princ.h"
diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index 909e855554..7699f36f8d 100644
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -56,7 +56,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "mdrun.h"
 #include "gromacs/random/random.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gmx_ana.h"
 
 static void insert_ion(int nsa, int *nwater,
diff --git a/src/gromacs/gmxana/gmx_genpr.c b/src/gromacs/gmxana/gmx_genpr.c
index 71d2a20772..4d2891cc13 100644
--- a/src/gromacs/gmxana/gmx_genpr.c
+++ b/src/gromacs/gmxana/gmx_genpr.c
@@ -48,7 +48,7 @@
 #include "gromacs/utility/futil.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_gyrate.c b/src/gromacs/gmxana/gmx_gyrate.c
index 6ca8bbff71..0ffb34ead5 100644
--- a/src/gromacs/gmxana/gmx_gyrate.c
+++ b/src/gromacs/gmxana/gmx_gyrate.c
@@ -47,7 +47,7 @@
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/xvgr.h"
 #include "viewit.h"
 #include "princ.h"
diff --git a/src/gromacs/gmxana/gmx_h2order.c b/src/gromacs/gmxana/gmx_h2order.c
index 7c23c3d9db..7a47f5c412 100644
--- a/src/gromacs/gmxana/gmx_h2order.c
+++ b/src/gromacs/gmxana/gmx_h2order.c
@@ -51,7 +51,7 @@
 #include "viewit.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gmx_ana.h"
 #include "gromacs/fileio/trxio.h"
 
diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index 79a46cb57b..5c28edf3d9 100644
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -47,7 +47,7 @@
 #include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/utility/fatalerror.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/fileio/xvgr.h"
diff --git a/src/gromacs/gmxana/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
index aa7fd92db9..21630d3526 100644
--- a/src/gromacs/gmxana/gmx_helix.c
+++ b/src/gromacs/gmxana/gmx_helix.c
@@ -50,7 +50,6 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "txtdump.h"
 #include "typedefs.h"
diff --git a/src/gromacs/gmxana/gmx_helixorient.c b/src/gromacs/gmxana/gmx_helixorient.c
index 503c2e7016..6481cd3ed0 100644
--- a/src/gromacs/gmxana/gmx_helixorient.c
+++ b/src/gromacs/gmxana/gmx_helixorient.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gstat.h"
 #include "gmx_ana.h"
 
diff --git a/src/gromacs/gmxana/gmx_hydorder.c b/src/gromacs/gmxana/gmx_hydorder.c
index 165f388513..d57a40d998 100644
--- a/src/gromacs/gmxana/gmx_hydorder.c
+++ b/src/gromacs/gmxana/gmx_hydorder.c
@@ -46,7 +46,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "binsearch.h"
diff --git a/src/gromacs/gmxana/gmx_make_edi.c b/src/gromacs/gmxana/gmx_make_edi.c
index d376119b95..7340e853cb 100644
--- a/src/gromacs/gmxana/gmx_make_edi.c
+++ b/src/gromacs/gmxana/gmx_make_edi.c
@@ -58,7 +58,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "txtdump.h"
 #include "eigio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 
 typedef struct
diff --git a/src/gromacs/gmxana/gmx_make_ndx.c b/src/gromacs/gmxana/gmx_make_ndx.c
index 9e3d47739d..3e48c99a26 100644
--- a/src/gromacs/gmxana/gmx_make_ndx.c
+++ b/src/gromacs/gmxana/gmx_make_ndx.c
@@ -45,9 +45,8 @@
 #include "macros.h"
 #include "gromacs/fileio/confio.h"
 #include "typedefs.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/topology/block.h"
diff --git a/src/gromacs/gmxana/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.c
index 1d0473fdcc..46ea9a0a7a 100644
--- a/src/gromacs/gmxana/gmx_mdmat.c
+++ b/src/gromacs/gmxana/gmx_mdmat.c
@@ -51,7 +51,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/pbcutil/rmpbc.h"
diff --git a/src/gromacs/gmxana/gmx_mindist.c b/src/gromacs/gmxana/gmx_mindist.c
index 787a6b0d09..c13e907598 100644
--- a/src/gromacs/gmxana/gmx_mindist.c
+++ b/src/gromacs/gmxana/gmx_mindist.c
@@ -51,7 +51,7 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/pbcutil/rmpbc.h"
diff --git a/src/gromacs/gmxana/gmx_morph.c b/src/gromacs/gmxana/gmx_morph.c
index dadb1590f9..e36ebeab79 100644
--- a/src/gromacs/gmxana/gmx_morph.c
+++ b/src/gromacs/gmxana/gmx_morph.c
@@ -41,7 +41,7 @@
 #include "macros.h"
 #include "gromacs/fileio/confio.h"
 #include "viewit.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gmx_ana.h"
 #include "gromacs/fileio/trxio.h"
 
diff --git a/src/gromacs/gmxana/gmx_msd.c b/src/gromacs/gmxana/gmx_msd.c
index bfdbac55ae..0692168a8b 100644
--- a/src/gromacs/gmxana/gmx_msd.c
+++ b/src/gromacs/gmxana/gmx_msd.c
@@ -44,7 +44,7 @@
 #include "macros.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "typedefs.h"
 #include "viewit.h"
 #include "gstat.h"
diff --git a/src/gromacs/gmxana/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
index 5497dfd098..7e2b5f8bde 100644
--- a/src/gromacs/gmxana/gmx_nmeig.c
+++ b/src/gromacs/gmxana/gmx_nmeig.c
@@ -45,7 +45,6 @@
 #include "macros.h"
 #include "copyrite.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
 #include "gstat.h"
 #include "txtdump.h"
 #include "eigio.h"
diff --git a/src/gromacs/gmxana/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.c
index 4ddf1300ca..f496b4d4d0 100644
--- a/src/gromacs/gmxana/gmx_nmens.c
+++ b/src/gromacs/gmxana/gmx_nmens.c
@@ -48,7 +48,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/gmx_nmtraj.c b/src/gromacs/gmxana/gmx_nmtraj.c
index b5edf8b564..4275f9cc87 100644
--- a/src/gromacs/gmxana/gmx_nmtraj.c
+++ b/src/gromacs/gmxana/gmx_nmtraj.c
@@ -49,7 +49,6 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
index 91f90383ae..b316179423 100644
--- a/src/gromacs/gmxana/gmx_order.c
+++ b/src/gromacs/gmxana/gmx_order.c
@@ -48,7 +48,7 @@
 #include "viewit.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/confio.h"
diff --git a/src/gromacs/gmxana/gmx_polystat.c b/src/gromacs/gmxana/gmx_polystat.c
index 44fe45d299..7d6cacd7ae 100644
--- a/src/gromacs/gmxana/gmx_polystat.c
+++ b/src/gromacs/gmxana/gmx_polystat.c
@@ -46,7 +46,7 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "macros.h"
 #include "gromacs/fileio/xvgr.h"
 #include "viewit.h"
diff --git a/src/gromacs/gmxana/gmx_potential.c b/src/gromacs/gmxana/gmx_potential.c
index 163522eacd..4957f6eab4 100644
--- a/src/gromacs/gmxana/gmx_potential.c
+++ b/src/gromacs/gmxana/gmx_potential.c
@@ -52,7 +52,7 @@
 #include "viewit.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gmx_ana.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/gmx_principal.c b/src/gromacs/gmxana/gmx_principal.c
index a46e1826a2..72db5d6ba5 100644
--- a/src/gromacs/gmxana/gmx_principal.c
+++ b/src/gromacs/gmxana/gmx_principal.c
@@ -47,7 +47,7 @@
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "princ.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "txtdump.h"
diff --git a/src/gromacs/gmxana/gmx_rama.c b/src/gromacs/gmxana/gmx_rama.c
index 6cfe0c4997..ab57c674cc 100644
--- a/src/gromacs/gmxana/gmx_rama.c
+++ b/src/gromacs/gmxana/gmx_rama.c
@@ -50,7 +50,6 @@
 #include "gromacs/math/units.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
-#include "index.h"
 #include "nrama.h"
 #include "gmx_ana.h"
 
diff --git a/src/gromacs/gmxana/gmx_rdf.c b/src/gromacs/gmxana/gmx_rdf.c
index 58c755afa1..94f39ab1e0 100644
--- a/src/gromacs/gmxana/gmx_rdf.c
+++ b/src/gromacs/gmxana/gmx_rdf.c
@@ -49,7 +49,7 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "nrnb.h"
 #include "coulomb.h"
 #include "gstat.h"
diff --git a/src/gromacs/gmxana/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
index ca69a60ab5..9776ea4af5 100644
--- a/src/gromacs/gmxana/gmx_rms.c
+++ b/src/gromacs/gmxana/gmx_rms.c
@@ -48,7 +48,7 @@
 #include "copyrite.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "princ.h"
diff --git a/src/gromacs/gmxana/gmx_rmsdist.c b/src/gromacs/gmxana/gmx_rmsdist.c
index 4c85111ffb..4c190b3bfc 100644
--- a/src/gromacs/gmxana/gmx_rmsdist.c
+++ b/src/gromacs/gmxana/gmx_rmsdist.c
@@ -50,7 +50,7 @@
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/math/vec.h"
 #include "macros.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/fileio/xvgr.h"
 #include "viewit.h"
diff --git a/src/gromacs/gmxana/gmx_rmsf.c b/src/gromacs/gmxana/gmx_rmsf.c
index 45e24b622c..d882951db3 100644
--- a/src/gromacs/gmxana/gmx_rmsf.c
+++ b/src/gromacs/gmxana/gmx_rmsf.c
@@ -47,7 +47,7 @@
 #include "viewit.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/gmx_rotacf.c b/src/gromacs/gmxana/gmx_rotacf.c
index 17c92c2c4c..17af340ff7 100644
--- a/src/gromacs/gmxana/gmx_rotacf.c
+++ b/src/gromacs/gmxana/gmx_rotacf.c
@@ -43,7 +43,7 @@
 
 #include "typedefs.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "macros.h"
 #include "gstat.h"
 #include "gromacs/math/vec.h"
diff --git a/src/gromacs/gmxana/gmx_rotmat.c b/src/gromacs/gmxana/gmx_rotmat.c
index c1844bd62f..4fcbb79f2e 100644
--- a/src/gromacs/gmxana/gmx_rotmat.c
+++ b/src/gromacs/gmxana/gmx_rotmat.c
@@ -45,7 +45,7 @@
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/xvgr.h"
 #include "viewit.h"
 #include "gromacs/pbcutil/rmpbc.h"
diff --git a/src/gromacs/gmxana/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
index 75730a68f8..a41a8dd18a 100644
--- a/src/gromacs/gmxana/gmx_sans.c
+++ b/src/gromacs/gmxana/gmx_sans.c
@@ -41,7 +41,7 @@
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "copyrite.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gstat.h"
 #include "gmx_ana.h"
 #include "nsfactor.h"
diff --git a/src/gromacs/gmxana/gmx_sorient.c b/src/gromacs/gmxana/gmx_sorient.c
index 1e1f75cd8a..8f94c4175a 100644
--- a/src/gromacs/gmxana/gmx_sorient.c
+++ b/src/gromacs/gmxana/gmx_sorient.c
@@ -43,7 +43,7 @@
 #include "gromacs/math/vec.h"
 #include "viewit.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_spatial.c b/src/gromacs/gmxana/gmx_spatial.c
index 9293e30f6c..640541c090 100644
--- a/src/gromacs/gmxana/gmx_spatial.c
+++ b/src/gromacs/gmxana/gmx_spatial.c
@@ -45,7 +45,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
 #include "gmx_ana.h"
diff --git a/src/gromacs/gmxana/gmx_spol.c b/src/gromacs/gmxana/gmx_spol.c
index afc8560e8e..e526dc1062 100644
--- a/src/gromacs/gmxana/gmx_spol.c
+++ b/src/gromacs/gmxana/gmx_spol.c
@@ -42,7 +42,7 @@
 #include "gstat.h"
 #include "viewit.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/math/units.h"
diff --git a/src/gromacs/gmxana/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.c
index 2a000147f4..8435a86280 100644
--- a/src/gromacs/gmxana/gmx_tcaf.c
+++ b/src/gromacs/gmxana/gmx_tcaf.c
@@ -49,7 +49,7 @@
 #include "macros.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/units.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "txtdump.h"
diff --git a/src/gromacs/gmxana/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.c
index 3f4a2e0e4d..b018260593 100644
--- a/src/gromacs/gmxana/gmx_traj.c
+++ b/src/gromacs/gmxana/gmx_traj.c
@@ -48,7 +48,7 @@
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/xvgr.h"
 #include "viewit.h"
 #include "gromacs/fileio/tpxio.h"
diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
index ce279a078f..fee1ce8020 100644
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.c
@@ -56,7 +56,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
 #include "names.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/xvgr.h"
diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
index 62726f169b..2c52f8e85e 100644
--- a/src/gromacs/gmxana/gmx_trjconv.c
+++ b/src/gromacs/gmxana/gmx_trjconv.c
@@ -54,7 +54,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
 #include "names.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/fileio/xtcio.h"
 #include "viewit.h"
diff --git a/src/gromacs/gmxana/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.c
index 9f17214b96..a9c2622785 100644
--- a/src/gromacs/gmxana/gmx_trjorder.c
+++ b/src/gromacs/gmxana/gmx_trjorder.c
@@ -49,7 +49,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/xvgr.h"
 
 #include "gromacs/pbcutil/rmpbc.h"
diff --git a/src/gromacs/gmxana/gmx_vanhove.c b/src/gromacs/gmxana/gmx_vanhove.c
index 640d786db9..8d773d9109 100644
--- a/src/gromacs/gmxana/gmx_vanhove.c
+++ b/src/gromacs/gmxana/gmx_vanhove.c
@@ -48,7 +48,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/utility/futil.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "typedefs.h"
 #include "gromacs/fileio/xvgr.h"
 #include "viewit.h"
diff --git a/src/gromacs/gmxana/gmx_velacc.c b/src/gromacs/gmxana/gmx_velacc.c
index 1a86e56b28..4103fc84f6 100644
--- a/src/gromacs/gmxana/gmx_velacc.c
+++ b/src/gromacs/gmxana/gmx_velacc.c
@@ -49,7 +49,7 @@
 #include "macros.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/units.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "txtdump.h"
diff --git a/src/gromacs/gmxana/gmx_wheel.c b/src/gromacs/gmxana/gmx_wheel.c
index 25768eff35..146756b7cd 100644
--- a/src/gromacs/gmxana/gmx_wheel.c
+++ b/src/gromacs/gmxana/gmx_wheel.c
@@ -47,7 +47,6 @@
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
 #include "gstat.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gmx_ana.h"
diff --git a/src/gromacs/gmxana/gstat.h b/src/gromacs/gmxana/gstat.h
index 959a86d937..8c9895a855 100644
--- a/src/gromacs/gmxana/gstat.h
+++ b/src/gromacs/gmxana/gstat.h
@@ -38,9 +38,9 @@
 #define GMX_GMXANA_GSTAT_H
 
 #include "../legacyheaders/typedefs.h"
-#include "../commandline/pargs.h"
 #include "../legacyheaders/oenv.h"
-#include "../legacyheaders/index.h"
+#include "../commandline/pargs.h"
+#include "../topology/index.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/gmxana/hxprops.c b/src/gromacs/gmxana/hxprops.c
index 5a999cec66..776b26ff44 100644
--- a/src/gromacs/gmxana/hxprops.c
+++ b/src/gromacs/gmxana/hxprops.c
@@ -45,7 +45,7 @@
 #include "macros.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "hxprops.h"
 #include "gromacs/utility/smalloc.h"
 #include "bondf.h"
diff --git a/src/gromacs/gmxana/nsfactor.h b/src/gromacs/gmxana/nsfactor.h
index ebe6b80874..c833a5521d 100644
--- a/src/gromacs/gmxana/nsfactor.h
+++ b/src/gromacs/gmxana/nsfactor.h
@@ -36,7 +36,6 @@
 #ifndef _nsfactor_h
 #define _nsfactor_h
 
-#include "gromacs/legacyheaders/index.h"
 #include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/legacyheaders/types/simple.h"
 
diff --git a/src/gromacs/gmxana/sfactor.c b/src/gromacs/gmxana/sfactor.c
index fdc251882d..e6e5a35b34 100644
--- a/src/gromacs/gmxana/sfactor.c
+++ b/src/gromacs/gmxana/sfactor.c
@@ -44,7 +44,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
 #include "macros.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
diff --git a/src/gromacs/gmxana/sfactor.h b/src/gromacs/gmxana/sfactor.h
index 6eae788116..d9099a8bd3 100644
--- a/src/gromacs/gmxana/sfactor.h
+++ b/src/gromacs/gmxana/sfactor.h
@@ -37,7 +37,6 @@
 #ifndef _sfactor_h
 #define _sfactor_h
 
-#include "index.h"
 #include "types/simple.h"
 #include "../math/gmxcomplex.h"
 #include "oenv.h"
diff --git a/src/gromacs/gmxpreprocess/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
index f0a69ab6ff..3dfbaa48bd 100644
--- a/src/gromacs/gmxpreprocess/gen_vsite.c
+++ b/src/gromacs/gmxpreprocess/gen_vsite.c
@@ -49,7 +49,7 @@
 #include "gromacs/math/vec.h"
 #include "toputil.h"
 #include "gromacs/math/units.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "names.h"
 #include "gromacs/utility/futil.h"
 #include "gpp_atomtype.h"
diff --git a/src/gromacs/gmxpreprocess/grompp.c b/src/gromacs/gmxpreprocess/grompp.c
index 1cfeba8e7b..2eef5b7b63 100644
--- a/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@ -62,7 +62,6 @@
 #include "gromacs/gmxpreprocess/sortwater.h"
 #include "convparm.h"
 #include "warninp.h"
-#include "index.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/tpxio.h"
diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.c b/src/gromacs/gmxpreprocess/pdb2gmx.c
index db0a541256..883d5b79c3 100644
--- a/src/gromacs/gmxpreprocess/pdb2gmx.c
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.c
@@ -62,7 +62,7 @@
 #include "gromacs/gmxlib/conformation-utilities.h"
 #include "genhydro.h"
 #include "readinp.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "fflibutil.h"
 #include "macros.h"
 
@@ -70,6 +70,7 @@
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/topology/atomprop.h"
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index f660c51f1f..a71f273c87 100644
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -57,7 +57,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gen_ad.h"
 #include "gromacs/fileio/filenm.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gen_vsite.h"
 #include "add_par.h"
 #include "toputil.h"
diff --git a/src/gromacs/gmxpreprocess/protonate.c b/src/gromacs/gmxpreprocess/protonate.c
index 7f2970bb28..5f10cc499d 100644
--- a/src/gromacs/gmxpreprocess/protonate.c
+++ b/src/gromacs/gmxpreprocess/protonate.c
@@ -50,7 +50,7 @@
 #include "genhydro.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/math/vec.h"
 #include "hackblock.h"
 
diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 3d560b9330..b8e9e6d9b8 100644
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -46,13 +46,12 @@
 #include "gromacs/math/units.h"
 #include "names.h"
 #include "macros.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "readinp.h"
 #include "warninp.h"
 #include "readir.h"
 #include "toputil.h"
-#include "index.h"
 #include "network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
diff --git a/src/gromacs/gmxpreprocess/readpull.c b/src/gromacs/gmxpreprocess/readpull.c
index da3dedec03..0e9706a7ae 100644
--- a/src/gromacs/gmxpreprocess/readpull.c
+++ b/src/gromacs/gmxpreprocess/readpull.c
@@ -49,7 +49,6 @@
 #include "names.h"
 #include "gromacs/utility/fatalerror.h"
 #include "macros.h"
-#include "index.h"
 #include "readinp.h"
 #include "readir.h"
 #include "mdatoms.h"
diff --git a/src/gromacs/gmxpreprocess/vsite_parm.c b/src/gromacs/gmxpreprocess/vsite_parm.c
index 773266ae92..6b8daa9919 100644
--- a/src/gromacs/gmxpreprocess/vsite_parm.c
+++ b/src/gromacs/gmxpreprocess/vsite_parm.c
@@ -50,7 +50,6 @@
 #include "gromacs/math/vec.h"
 #include "toputil.h"
 #include "gromacs/math/units.h"
-#include "index.h"
 #include "names.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/cstringutil.h"
diff --git a/src/gromacs/gmxpreprocess/xlate.c b/src/gromacs/gmxpreprocess/xlate.c
index f98cc2a09b..faf148c120 100644
--- a/src/gromacs/gmxpreprocess/xlate.c
+++ b/src/gromacs/gmxpreprocess/xlate.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "typedefs.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "fflibutil.h"
 #include "hackblock.h"
 #include "xlate.h"
diff --git a/src/gromacs/gmxpreprocess/xlate.h b/src/gromacs/gmxpreprocess/xlate.h
index 892569fb6c..83d667b0b3 100644
--- a/src/gromacs/gmxpreprocess/xlate.h
+++ b/src/gromacs/gmxpreprocess/xlate.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_XLATE_H
 #define GMX_GMXPREPROCESS_XLATE_H
 
-#include "index.h"
+#include "gromacs/topology/index.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/gromacs/pulling/pull.c b/src/gromacs/pulling/pull.c
index 265749eeee..77a773c9e4 100644
--- a/src/gromacs/pulling/pull.c
+++ b/src/gromacs/pulling/pull.c
@@ -44,7 +44,6 @@
 #include <string.h>
 
 #include "gromacs/utility/futil.h"
-#include "index.h"
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "network.h"
diff --git a/src/gromacs/pulling/pullutil.c b/src/gromacs/pulling/pullutil.c
index 6cd0cef2ff..1b13d4eabc 100644
--- a/src/gromacs/pulling/pullutil.c
+++ b/src/gromacs/pulling/pullutil.c
@@ -48,7 +48,6 @@
 #include "names.h"
 #include "gromacs/utility/fatalerror.h"
 #include "macros.h"
-#include "index.h"
 #include "gromacs/fileio/confio.h"
 #include "network.h"
 #include "gromacs/pbcutil/pbc.h"
diff --git a/src/gromacs/selection/indexutil.cpp b/src/gromacs/selection/indexutil.cpp
index b2f5b053bf..f921caeaac 100644
--- a/src/gromacs/selection/indexutil.cpp
+++ b/src/gromacs/selection/indexutil.cpp
@@ -47,9 +47,8 @@
 #include <string>
 #include <vector>
 
-#include "gromacs/legacyheaders/index.h"
-
 #include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.c
index 47c703efa5..ce319bff89 100644
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.c
@@ -46,7 +46,7 @@
 #include "txtdump.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/units.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "names.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/fileio/gmxfio.h"
diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.c
index 16becfb6c3..21204a11b7 100644
--- a/src/gromacs/tools/convert_tpr.c
+++ b/src/gromacs/tools/convert_tpr.c
@@ -43,7 +43,7 @@
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/types/state.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "macros.h"
 #include "names.h"
 #include "gromacs/gmxpreprocess/readir.h"
diff --git a/src/gromacs/topology/CMakeLists.txt b/src/gromacs/topology/CMakeLists.txt
index fb900cfca0..ffc2379e83 100644
--- a/src/gromacs/topology/CMakeLists.txt
+++ b/src/gromacs/topology/CMakeLists.txt
@@ -40,6 +40,7 @@ set(TOPOLOGY_PUBLIC_HEADERS
     atoms.h
     block.h
     idef.h
+    index.h
     mtop_util.h
     symtab.h
     topology.h)
diff --git a/src/gromacs/topology/atomprop.cpp b/src/gromacs/topology/atomprop.cpp
index 519a5bb897..09cb30785b 100644
--- a/src/gromacs/topology/atomprop.cpp
+++ b/src/gromacs/topology/atomprop.cpp
@@ -45,8 +45,8 @@
 
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/index.h"
 #include "gromacs/math/utilities.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
diff --git a/src/gromacs/gmxlib/index.c b/src/gromacs/topology/index.cpp
similarity index 97%
rename from src/gromacs/gmxlib/index.c
rename to src/gromacs/topology/index.cpp
index 3adb8aca29..60bbef46d1 100644
--- a/src/gromacs/gmxlib/index.c
+++ b/src/gromacs/topology/index.cpp
@@ -34,6 +34,8 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gromacs/topology/index.h"
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
@@ -43,16 +45,17 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "macros.h"
-#include "names.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "index.h"
-#include "txtdump.h"
+#include <algorithm>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/block.h"
 #include "gromacs/topology/invblock.h"
+#include "gromacs/utility/common.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
@@ -182,8 +185,6 @@ static void
 p_status(const char **restype, int nres, const char **typenames, int ntypes)
 {
     int   i, j;
-    int   found;
-
     int * counter;
 
     snew(counter, ntypes);
@@ -193,7 +194,6 @@ p_status(const char **restype, int nres, const char **typenames, int ntypes)
     }
     for (i = 0; i < nres; i++)
     {
-        found = 0;
         for (j = 0; j < ntypes; j++)
         {
             if (!gmx_strcasecmp(restype[i], typenames[j]))
@@ -215,7 +215,7 @@ p_status(const char **restype, int nres, const char **typenames, int ntypes)
 }
 
 
-atom_id *
+static atom_id *
 mk_aid(t_atoms *atoms, const char ** restype, const char * typestring, int *nra, gmx_bool bMatch)
 /* Make an array of atom_ids for all atoms with residuetypes matching typestring, or the opposite if bMatch is false */
 {
@@ -371,7 +371,7 @@ typedef struct gmx_help_make_index_group
     /** The set of atom names that will be used to form this index group */
     const char **defining_atomnames;
     /** Size of the defining_atomnames array */
-    const int    num_defining_atomnames;
+    int          num_defining_atomnames;
     /** Name of this index group */
     const char  *group_name;
     /** Whether the above atom names name the atoms in the group, or
@@ -422,7 +422,7 @@ static void analyse_prot(const char ** restype, t_atoms *atoms,
 
     int         n, j;
     atom_id    *aid;
-    int         nra, nnpres, npres;
+    int         nra, npres;
     gmx_bool    match;
     char        ndx_name[STRLEN], *atnm;
     int         i;
@@ -580,7 +580,6 @@ static void analyse_prot(const char ** restype, t_atoms *atoms,
             if (nra > 0)
             {
                 add_grp(gb, gn, nra, aid, "SwapSC-CO");
-                nra = 0;
             }
         }
     }
@@ -612,7 +611,6 @@ gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char
 int
 gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype)
 {
-    int           i;
     int           found;
     const char *  p_oldtype;
 
@@ -643,8 +641,6 @@ gmx_residuetype_init(gmx_residuetype_t *prt)
     FILE                 *  db;
     char                    line[STRLEN];
     char                    resname[STRLEN], restype[STRLEN], dum[STRLEN];
-    char                 *  p;
-    int                     i;
     struct gmx_residuetype *rt;
 
     snew(rt, 1);
@@ -699,24 +695,21 @@ gmx_residuetype_get_alltypes(gmx_residuetype_t    rt,
                              const char ***       p_typenames,
                              int *                ntypes)
 {
-    int            i, j, n;
-    int            found;
+    int            i, n;
     const char **  my_typename;
-    char       *   p;
-
-    n = 0;
 
+    n           = 0;
     my_typename = NULL;
     for (i = 0; i < rt->n; i++)
     {
-        p     = rt->restype[i];
-        found = 0;
-        for (j = 0; j < n && !found; j++)
+        const char *const p      = rt->restype[i];
+        bool              bFound = false;
+        for (int j = 0; j < n && !bFound; j++)
         {
-            found = !gmx_strcasecmp(p, my_typename[j]);
+            assert(my_typename != NULL);
+            bFound = !gmx_strcasecmp(p, my_typename[j]);
         }
-
-        if (!found)
+        if (!bFound)
         {
             srenew(my_typename, n+1);
             my_typename[n] = p;
@@ -835,9 +828,7 @@ void analyse(t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool b
     const char    **  restype;
     int               nra;
     int               i, k;
-    size_t            j;
     int               ntypes;
-    char           *  p;
     const char     ** p_typename;
     int               iwater, iion;
     int               nwater, nion;
@@ -874,6 +865,7 @@ void analyse(t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool b
         found = 0;
         for (k = 0; k < ntypes && !found; k++)
         {
+            assert(p_typename != NULL);
             found = !strcmp(restype[i], p_typename[k]);
         }
         if (!found)
@@ -1008,7 +1000,7 @@ t_blocka *init_index(const char *gfile, char ***grpname)
     FILE      *in;
     t_blocka  *b;
     int        a, maxentries;
-    int        i, j, ng, nread;
+    int        i, j, ng;
     char       line[STRLEN], *pt, str[STRLEN];
 
     in = gmx_fio_fopen(gfile, "r");
@@ -1071,7 +1063,7 @@ t_blocka *init_index(const char *gfile, char ***grpname)
         snew(b->a, b->nra);
         for (i = 0; (i < b->nr); i++)
         {
-            nread         = fscanf(in, "%s%d", str, &ng);
+            GMX_IGNORE_RETURN_VALUE(fscanf(in, "%s%d", str, &ng));
             (*grpname)[i] = strdup(str);
             b->index[i+1] = b->index[i]+ng;
             if (b->index[i+1] > b->nra)
@@ -1080,7 +1072,7 @@ t_blocka *init_index(const char *gfile, char ***grpname)
             }
             for (j = 0; (j < ng); j++)
             {
-                nread               = fscanf(in, "%d", &a);
+                GMX_IGNORE_RETURN_VALUE(fscanf(in, "%d", &a));
                 b->a[b->index[i]+j] = a;
             }
         }
@@ -1329,7 +1321,7 @@ t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx)
     c->maxframe  = -1;
     for (i = 0; (i < c->clust->nra); i++)
     {
-        c->maxframe = max(c->maxframe, c->clust->a[i]);
+        c->maxframe = std::max(c->maxframe, c->clust->a[i]);
     }
     fprintf(fplog ? fplog : stdout,
             "There are %d clusters containing %d structures, highest framenr is %d\n",
diff --git a/src/gromacs/legacyheaders/index.h b/src/gromacs/topology/index.h
similarity index 96%
rename from src/gromacs/legacyheaders/index.h
rename to src/gromacs/topology/index.h
index 940dc0820b..91ec2ce8e1 100644
--- a/src/gromacs/legacyheaders/index.h
+++ b/src/gromacs/topology/index.h
@@ -34,13 +34,12 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
-#ifndef _index_h
-#define _index_h
+#ifndef GMX_TOPOLOGY_INDEX_H
+#define GMX_TOPOLOGY_INDEX_H
 
 #include <stdio.h>
 
-#include "types/simple.h"
+#include "../legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -96,13 +95,7 @@ typedef struct {
 
 t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx);
 
-typedef struct {
-    int    n;
-    char **name;
-} t_names;
-
-typedef struct gmx_residuetype *
-    gmx_residuetype_t;
+typedef struct gmx_residuetype *gmx_residuetype_t;
 
 int
 gmx_residuetype_init(gmx_residuetype_t *rt);
@@ -163,4 +156,4 @@ int find_group(char s[], int ngrps, char **grpname);
 }
 #endif
 
-#endif  /* _index_h */
+#endif
diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index e320584225..f461964003 100644
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -46,7 +46,6 @@
 #include "mdebin.h"
 #include "nrnb.h"
 #include "calcmu.h"
-#include "index.h"
 #include "vsite.h"
 #include "update.h"
 #include "ns.h"
diff --git a/src/programs/mdrun/membed.c b/src/programs/mdrun/membed.c
index 04ebc2a94d..0bd722ab1f 100644
--- a/src/programs/mdrun/membed.c
+++ b/src/programs/mdrun/membed.c
@@ -45,7 +45,7 @@
 #include "macros.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/essentialdynamics/edsam.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "names.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/fileio/tpxio.h"
diff --git a/src/programs/view/filter.cpp b/src/programs/view/filter.cpp
index 8534a3a765..a888854618 100644
--- a/src/programs/view/filter.cpp
+++ b/src/programs/view/filter.cpp
@@ -45,10 +45,9 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "xdlghi.h"
 #include "dialogs.h"
-#include "index.h"
 #include "gromacs/utility/fatalerror.h"
 
 t_filter *init_filter(t_atoms *atoms, const char *fn, int natom_trx)
diff --git a/tests/CppCheck.cmake b/tests/CppCheck.cmake
index cedcc1dfe6..8ca224cb9d 100644
--- a/tests/CppCheck.cmake
+++ b/tests/CppCheck.cmake
@@ -98,6 +98,7 @@ if (CPPCHECK_EXECUTABLE AND UNIX)
         --suppress=unnecessaryForwardDeclaration
         --suppress=invalidscanf:src/gromacs/fileio/matio.cpp
         --suppress=invalidscanf:src/gromacs/fileio/xvgr.cpp
+        --suppress=invalidscanf:src/gromacs/topology/index.cpp
         --suppress=invalidscanf:src/gromacs/gmxpreprocess/pdb2top.cpp)
 
     # This list will hold the list of all files with cppcheck errors