Merge release-5-0 into master

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / pdb2top.cpp

diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index befb6a6a7ff01f3a912d874a5893680b7dbbf242..7b08b863c42bc69caf7e78d21223ceba7401bb0b 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -42,12 +42,9 @@
 #include <math.h>
 #include <ctype.h>
 
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/math/vec.h"
 #include "macros.h"
-#include "symtab.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
 #include "pdb2top.h"
 #include "gpp_nextnb.h"
 #include "topdirs.h"
@@ -57,11 +54,9 @@
 #include "resall.h"
 #include "topio.h"
 #include "gromacs/utility/cstringutil.h"
-#include "physics.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gen_ad.h"
 #include "gromacs/fileio/filenm.h"
-#include "index.h"
 #include "gen_vsite.h"
 #include "add_par.h"
 #include "toputil.h"
@@ -69,8 +64,12 @@
 #include "copyrite.h"
 
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 
 /* this must correspond to enum in pdb2top.h */
 const char *hh[ehisNR]   = { "HISD", "HISE", "HISH", "HIS1" };
@@ -443,7 +442,7 @@ void choose_watermodel(const char *wmsel, const char *ffdir,
 }
 
 static int name2type(t_atoms *at, int **cgnr,
-                     t_restp restp[], gmx_residuetype_t rt)
+                     t_restp restp[], gmx_residuetype_t *rt)
 {
     int         i, j, prevresind, resind, i0, prevcg, cg, curcg;
     char       *name;
@@ -1426,7 +1425,7 @@ void match_atomnames_with_rtp(t_restp restp[], t_hackblock hb[],
 }
 
 #define NUM_CMAP_ATOMS 5
-static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuetype_t rt)
+static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuetype_t *rt)
 {
     int         residx, i, j, k;
     const char *ptr;
@@ -1540,7 +1539,7 @@ void pdb2top(FILE *top_file, char *posre_fn, char *molname,
     int              *vsite_type;
     int               i, nmissat;
     int               bts[ebtsNR];
-    gmx_residuetype_t rt;
+    gmx_residuetype_t*rt;
 
     init_plist(plist);
     gmx_residuetype_init(&rt);