#include <stdlib.h>
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/strdb.h"
-#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/dir_separator.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
static int strip_dssp(char *dsspfile, int nres,
"Even newer versions (which at the time of writing are not yet released)",
"are assumed to have the same syntax as 2.0.0.[PAR]",
"The structure assignment for each residue and time is written to an",
- "[TT].xpm[tt] matrix file. This file can be visualized with for instance",
+ "[REF].xpm[ref] matrix file. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [TT]xpm2ps[tt].",
- "Individual chains are separated by light grey lines in the [TT].xpm[tt] and",
+ "Individual chains are separated by light grey lines in the [REF].xpm[ref] and",
"postscript files.",
"The number of residues with each secondary structure type and the",
"total secondary structure ([TT]-sss[tt]) count as a function of",