* 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 "protonate.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "protonate.h"
#include <math.h>
-#include "string2.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "genhydro.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "index.h"
-#include "vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/math/vec.h"
#include "hackblock.h"
+#include "gromacs/utility/fatalerror.h"
+
int gmx_protonate(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] reads (a) conformation(s) and adds all missing",
- "hydrogens as defined in [TT]gmx2.ff/aminoacids.hdb[tt]. If only [TT]-s[tt] is",
+ "hydrogens as defined in [TT]oplsaa.ff/aminoacids.hdb[tt]. If only [TT]-s[tt] is",
"specified, this conformation will be protonated, if also [TT]-f[tt]",
"is specified, the conformation(s) will be read from this file, ",
"which can be either a single conformation or a trajectory.",