From: David van der Spoel <spoel@xray.bmc.uu.se>
Date: Tue, 9 Sep 2014 05:55:17 +0000 (+0200)
Subject: Remove .tpa, .tpb, .tpx, .trj files. Part of #1500.
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?p=alexxy%2Fgromacs.git;a=commitdiff_plain;h=b2b75d45c43c98cf1362e0125381bfc6f0a85782

Remove .tpa, .tpb, .tpx, .trj files. Part of #1500.

Change-Id: Ia055cbf5311bf8780ca826c767207e5172d1b7e2
---

diff --git a/docs/manual/files.tex b/docs/manual/files.tex
index 1fae94e989..af67d4a6ec 100644
--- a/docs/manual/files.tex
+++ b/docs/manual/files.tex
@@ -54,7 +54,7 @@
 \tt     conf & \tt esp & Asc & \tt -c & Coordinate file in ESPResSo format \\[-0.1ex]
 \tt     conf & \tt g96 & Asc & \tt -c & Coordinate file in Gromos-96 format \\[-0.1ex]
 \tt     conf & \tt gro & Asc & \tt -c & Coordinate file in Gromos-87 format \\[-0.1ex]
-\tt     conf & \tt gro &     & \tt -c & Structure: \tt gro g96 pdb esp tpr tpb tpa \\[-0.1ex]
+\tt     conf & \tt gro &     & \tt -c & Structure: \tt gro g96 pdb esp tpr \\[-0.1ex]
 \tt      out & \tt gro &     & \tt -o & Structure: \tt gro g96 pdb esp \\[-0.1ex]
 \tt    polar & \tt hdb & Asc & \tt    & Hydrogen data base \\[-0.1ex]
 \tt   topinc & \tt itp & Asc & \tt    & Include file for topology \\[-0.1ex]
@@ -70,16 +70,14 @@
 \tt  residue & \tt rtp & Asc & \tt    & Residue Type file used by {\tt pdb2gmx} \\[-0.1ex]
 \tt      doc & \tt tex & Asc & \tt -o & LaTeX file \\[-0.1ex]
 \tt    topol & \tt top & Asc & \tt -p & Topology file \\[-0.1ex]
-\tt    topol & \tt tpb & Bin & \tt -s & Binary run input file \\[-0.1ex]
-\tt    topol & \tt tpr &     & \tt -s & Generic run input: \tt tpr tpb tpa \\[-0.1ex]
-\tt    topol & \tt tpr &     & \tt -s & Structure+mass(db): \tt tpr tpb tpa gro g96 pdb \\[-0.1ex]
+\tt    topol & \tt tpr &     & \tt -s & Generic run input: \tt tpr \\[-0.1ex]
+\tt    topol & \tt tpr &     & \tt -s & Structure+mass(db): \tt tpr gro g96 pdb \\[-0.1ex]
 \tt    topol & \tt tpr & xdr & \tt -s & Portable xdr run input file \\[-0.1ex]
-\tt     traj & \tt trj & Bin & \tt    & Trajectory file (architecture specific) \\[-0.1ex]
-\tt     traj & \tt trr &     & \tt    & Full precision trajectory: \tt trr trj cpt \\[-0.1ex]
+\tt     traj & \tt trr &     & \tt    & Full precision trajectory: \tt trr cpt \\[-0.1ex]
 \tt     traj & \tt trr & xdr & \tt    & Trajectory in portable xdr format \\[-0.1ex]
 \tt     root & \tt xpm & Asc & \tt    & X PixMap compatible matrix file \\[-0.1ex]
-\tt     traj & \tt xtc &     & \tt -f & Trajec., input: \tt xtc trr trj cpt gro g96 pdb \\[-0.1ex]
-\tt     traj & \tt xtc &     & \tt -f & Trajectory, output: \tt xtc trr trj gro g96 pdb \\[-0.1ex]
+\tt     traj & \tt xtc &     & \tt -f & Trajec., input: \tt xtc trr cpt gro g96 pdb \\[-0.1ex]
+\tt     traj & \tt xtc &     & \tt -f & Trajectory, output: \tt xtc trr gro g96 pdb \\[-0.1ex]
 \tt     traj & \tt xtc & xdr & \tt    & Compressed trajectory (portable xdr format) \\[-0.1ex]
 \tt    graph & \tt xvg & Asc & \tt -o & xvgr/xmgr file \\[-0.1ex]
 \dline
@@ -90,6 +88,6 @@
 
 % LocalWords:  lccX atomtp atp Asc Atomtype pdb gmx eiwit brk Brookhaven cpt tm
 % LocalWords:  xdr nnnice dat dlg ngmx sam edi edo ener edr ene ent eps conf ss
-% LocalWords:  PostScript ESPResSo gtraj Gromos gro tpr tpb tpa hdb topinc itp
-% LocalWords:  grompp mdp mtx ndx rtp tex LaTeX topol traj trj trr xpm PixMap
+% LocalWords:  PostScript ESPResSo gtraj Gromos gro tpr hdb topinc itp
+% LocalWords:  grompp mdp mtx ndx rtp tex LaTeX topol traj trr xpm PixMap
 % LocalWords:  xtc Trajec xvg xvgr xmgr ps
diff --git a/docs/old-html/links.dat b/docs/old-html/links.dat
index 8ee9ba7b0c..01ee831ccc 100644
--- a/docs/old-html/links.dat
+++ b/docs/old-html/links.dat
@@ -19,10 +19,7 @@ rtp
 tex
 top
 tng
-tpa
-tpb
 tpr
-trj
 trr
 xpm
 xtc
diff --git a/docs/old-html/online/files.html b/docs/old-html/online/files.html
index ee57c53221..e458217867 100644
--- a/docs/old-html/online/files.html
+++ b/docs/old-html/online/files.html
@@ -18,14 +18,10 @@
 <dt><b>Generic structure formats:</b>
 <a href="gro.html">gro</a>,
 <a href="g96.html">g96</a>,
-<a href="pdb.html">pdb</a>,
-<a href="tpr.html">tpr</a>,
-<a href="tpb.html">tpb</a> or
-<a href="tpa.html">tpa</a>
+<a href="pdb.html">pdb</a>, or
+<a href="tpr.html">tpr</a>
 <dt><b>Structure+mass(db):</b>
 <a href="tpr.html">tpr</a>,
-<a href="tpb.html">tpb</a>,
-<a href="tpa.html">tpa</a>,
 <a href="gro.html">gro</a>,
 <a href="g96.html">g96</a> or
 <a href="pdb.html">pdb</a>.
@@ -45,35 +41,26 @@ When gro or pdb is used approximate masses will be read from the mass database.
 <dd><dl compact>
 <dt><a href="tpr.html">tpr</a> <dd>system topology, parameters, coordinates 
 and velocities (binary, portable)
-<dt><a href="tpa.html">tpa</a> <dd>system topology, parameters, coordinates 
-and velocities (ascii)
-<dt><a href="tpb.html">tpb</a> <dd>system topology, parameters, coordinates 
-and velocities (binary)
 <dt><b>Generic run input file formats:</b>
-<a href="tpr.html">tpr</a>,
-<a href="tpb.html">tpb</a> or
-<a href="tpa.html">tpa</a>
+<a href="tpr.html">tpr</a>
 
 </dl>
 
 <br><dt><h3>Trajectory files</h3>
 <dd><dl compact>
 <dt><a href="tng.html">tng</a> <dd>Any kind of data (compressed, portable, any precision)
-<dt><a href="trj.html">trj</a> <dd>x, v and f (binary, full precision)
 <dt><a href="trr.html">trr</a> <dd>x, v and f (binary, full precision, portable)
 <dt><a href="xtc.html">xtc</a> <dd>x only (compressed, portable, any precision)
 <dt><a href="gro.html">gro</a> <dd>x and v (ascii, any precision)
 <dt><a href="g96.html">g96</a> <dd>x only (ascii, fixed high precision)
 <dt><a href="pdb.html">pdb</a> <dd>x only (ascii, reduced precision)
 <dt><b>Formats for full-precision data:</b>
-<a href="tng.html">tng</a>,
-<a href="trr.html">trr</a> or
-<a href="trj.html">trj</a>
+<a href="tng.html">tng</a> or
+<a href="trr.html">trr</a>
 <dt><b>Generic trajectory formats:</b>
 <a href="tng.html">tng</a>,
 <a href="xtc.html">xtc</a>,
 <a href="trr.html">trr</a>,
-<a href="trj.html">trj</a>,
 <a href="gro.html">gro</a>,
 <a href="g96.html">g96</a>,
 <a href="pdb.html">pdb</a> or
diff --git a/docs/old-html/online/getting_started.html b/docs/old-html/online/getting_started.html
index d9de09fad5..fcaf75c72d 100644
--- a/docs/old-html/online/getting_started.html
+++ b/docs/old-html/online/getting_started.html
@@ -183,8 +183,7 @@ not consider the use of index files.
 The next step is to combine the molecular structure (<TT><a href="gro.html">.gro</a></TT> file),
 topology (<TT><a href="top.html">.top</a></TT> file) MD-parameters (<TT><a href="mdp_opt.html">.mdp</a></TT> file) and 
 (optionally) the
-index file (<TT><a href="ndx.html">ndx</a></TT>) to generate a run input file (<TT><a href="tpr.html">.tpr</a></tt> extension or
-<TT><a href="tpb.html">.tpb</a></tt> if you don't have XDR).
+index file (<TT><a href="ndx.html">ndx</a></TT>) to generate a run input file (<TT><a href="tpr.html">.tpr</a></tt> extension.
 This file contains all information needed to start a simulation with GROMACS.
 The
 <a href="../programs/gmx-grompp.html">gmx grompp</a> program processes all
@@ -203,8 +202,7 @@ to start a run
 is the run input file (<TT><a href="tpr.html">.tpr</a></TT> file).
 The output files of 
 <TT><a href="../programs/gmx-mdrun.html">gmx mdrun</a></TT> are the
-trajectory file (<TT><a href="trr.html">.trr</a></TT> file
-or <TT><a href="trj.html">.trj</a></TT> if you don't have XDR) and a logfile (
+trajectory file (<TT><a href="trr.html">.trr</a></TT> file) and a logfile (
 <TT><a href="log.html">.log</A></TT> file).
 <P></P>
 
diff --git a/docs/old-html/online/mtx.html b/docs/old-html/online/mtx.html
index c023102238..6492e5db38 100644
--- a/docs/old-html/online/mtx.html
+++ b/docs/old-html/online/mtx.html
@@ -1,7 +1,7 @@
 <title>mtx file format</title>
 <H3>Description</H3>
 Files with the mtx file extension contain a matrix.
-The file format is identical to the <a href="trj.html">trj</a> format.
+The file format is identical to the <a href="trr.html">trr</a> format.
 Currently this file format is only used for hessian matrices,
 which are produced with <a href="../programs/gmx-mdrun.html">gmx mdrun</a> and read by
 <a href="../programs/gmx-nmeig.html">gmx nmeig</a>.
diff --git a/docs/old-html/online/options.html b/docs/old-html/online/options.html
index af9fc65727..a2e0cfa3cb 100644
--- a/docs/old-html/online/options.html
+++ b/docs/old-html/online/options.html
@@ -38,7 +38,7 @@ parameter is supplied the two others are also set to this value.
 <LI>
 All GROMACS programs can read compressed or g-zipped files. There
 might be a problem with reading compressed <tt>.xtc</tt>,
-<tt>.trr</tt> and <tt>.trj</tt> files, but these will not compress
+<tt>.trr</tt> files, but these will not compress
 very well anyway.
 <P>
 <LI>
diff --git a/docs/old-html/online/top.html b/docs/old-html/online/top.html
index 8bba16691f..67f6c174ff 100644
--- a/docs/old-html/online/top.html
+++ b/docs/old-html/online/top.html
@@ -2,7 +2,7 @@
 <H3>Description</H3>
 The top file extension stands for topology. It is an ascii file which is 
 read by <a href="../programs/gmx-grompp.html">gmx grompp</a> which processes it
-and creates a binary topology (<a href="tpb.html">.tpb file</a>).<br>
+and creates a binary topology (<a href="tpr.html">.tpr file</a>).<br>
 A sample file is included below:
 <pre>
 ;
diff --git a/docs/old-html/online/tpa.html b/docs/old-html/online/tpa.html
deleted file mode 100644
index 9002525fea..0000000000
--- a/docs/old-html/online/tpa.html
+++ /dev/null
@@ -1,19 +0,0 @@
-<title>tpa file format</title>
-<H3>Description</H3>
-The tpa file extension stands for binary run input file. This file contains 
-the starting structure of your simulation, The molecular topology and 
-all the simulation data. Because this file is in binary format it 
-cannot be read with a normal editor. To read a binary run input file type:
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -s topol.tpa
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -s topol.tpa | more
-</PRE>
-
-<p>
-You can also compare two tpa files using:
-<pre>
-% <a href="../programs/gmx-check.html">gmx check</a> -s1 top1 -s2 top2 | more
-</pre>
diff --git a/docs/old-html/online/tpb.html b/docs/old-html/online/tpb.html
deleted file mode 100644
index 4206296a66..0000000000
--- a/docs/old-html/online/tpb.html
+++ /dev/null
@@ -1,19 +0,0 @@
-<title>tpb file format</title>
-<h3>Description</h3>
-The tpb file extension stands for binary run input file. This file contains 
-the starting structure of your simulation, The molecular topology and 
-all the simulation data. Because this file is in binary format it 
-cannot be read with a normal editor. To read a binary run input file type:
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -s topol.tpb
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -s topol.tpb | more
-</PRE>
-
-<p>
-You can also compare two tpb files using:
-<pre>
-% <a href="../programs/gmx-check.html">gmx check</a> -s1 top1 -s2 top2 | more
-</pre>
diff --git a/docs/old-html/online/trj.html b/docs/old-html/online/trj.html
deleted file mode 100644
index 0077a8ed01..0000000000
--- a/docs/old-html/online/trj.html
+++ /dev/null
@@ -1,20 +0,0 @@
-<title>trj file format</title>
-<h3>Description</h3>
-Files with the trj file extension contain the trajectory of a simulation. 
-In this file all the coordinates, velocities, forces and energies are 
-printed as you told GROMACS in your mdp file. This file is in binary 
-format an can be read with <a href="../programs/gmx-dump.html">gmx dump</a>.
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -f traj.trj
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -f traj.trj | more
-</PRE>
-
-<p>
-You can also get a quick look in the contents of the file (number of 
-frames etc.) using:
-<PRE>
-% <a href="../programs/gmx-check.html">gmx check</a> -f traj.trj
-</PRE>
diff --git a/src/contrib/anaf.c b/src/contrib/anaf.c
index 0f5ab1a407..8267fea6b0 100644
--- a/src/contrib/anaf.c
+++ b/src/contrib/anaf.c
@@ -137,9 +137,9 @@ static void list_trn(char *fn)
 int main(int argc,char *argv[])
 {
   static char *desc[] = {
-    "[TT]gmxdump[tt] reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
-    "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]) or an energy",
-    "file ([TT].ene[tt]/[TT].edr[tt]) and prints that to standard",
+    "[TT]gmxdump[tt] reads a run input file ([TT].tpr[tt]),",
+    "a trajectory ([TT].trr[tt]/[TT].xtc[tt]) or an energy",
+    "file ([TT].edr[tt]) and prints that to standard",
     "output in a readable format. This program is essential for",
     "checking your run input file in case of problems.[PAR]"
   };
diff --git a/src/gromacs/commandline/tests/pargs.cpp b/src/gromacs/commandline/tests/pargs.cpp
index a7f4362732..55dc8b0c36 100644
--- a/src/gromacs/commandline/tests/pargs.cpp
+++ b/src/gromacs/commandline/tests/pargs.cpp
@@ -495,13 +495,13 @@ TEST_F(ParseCommonArgsTest, CompletesExtensionFromExistingFileWithDefaultFileNam
 {
     t_filenm          fnm[] = {
         { efTRX, "-f1", NULL,  ffREAD },
-        { efTPX, "-f2", "foo", ffREAD },
+        { efSTO, "-f2", "foo", ffREAD },
         { efTRX, "-f3", NULL,  ffREAD },
         { efSTX, "-f4", NULL,  ffREAD }
     };
     args_.append("test");
     std::string       expected1 = addFileArg("-f1", "1.trr", efNoExtension);
-    std::string       expected2 = addFileArg("-f2", ".tpa", efEmptyValue);
+    std::string       expected2 = addFileArg("-f2", ".pdb", efEmptyValue);
     std::string       expected3 = addFileArg("-f3", ".trr", efEmptyValue);
     std::string       expected4 = addFileArg(NULL, ".pdb", efEmptyValue);
     std::string       deffnm    = gmx::Path::stripExtension(expected3);
diff --git a/src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesLongFileOptions.xml b/src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesLongFileOptions.xml
index 64dcfe4606..8ac10f83fe 100644
--- a/src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesLongFileOptions.xml
+++ b/src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesLongFileOptions.xml
@@ -12,12 +12,11 @@ OPTIONS
 Options to specify input and output files:
 
  -f     [<.xtc/.trr/...>] (path/to/long/trajectory/name.xtc) (Input)
-     File name option with a long value: xtc trr cpt trj gro g96 pdb tng
+     File name option with a long value: xtc trr cpt gro g96 pdb tng
  -f2    [<.xtc/.trr/...>] (path/to/long/trajectory.xtc) (Input)
-     File name option with a long value: xtc trr cpt trj gro g96 pdb tng
+     File name option with a long value: xtc trr cpt gro g96 pdb tng
  -lib   [<.xtc/.trr/...>] (path/to/long/trajectory/name.xtc) (Input, Opt., Lib.)
-     File name option with a long value and type: xtc trr cpt trj gro g96 pdb
-     tng
+     File name option with a long value and type: xtc trr cpt gro g96 pdb tng
  -longfileopt [<.dat>] (deffile.dat) (Input, Opt.)
      File name option with a long name
  -longfileopt2 [<.dat>] (path/to/long/file/name.dat) (Input, Opt., Lib.)
diff --git a/src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesOptionTypes.xml b/src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesOptionTypes.xml
index c4abb113cf..d60500d2bf 100644
--- a/src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesOptionTypes.xml
+++ b/src/gromacs/commandline/tests/refdata/CommandLineHelpWriterTest_HandlesOptionTypes.xml
@@ -14,9 +14,9 @@ OPTIONS
 Options to specify input and output files:
 
  -f     [<.xtc/.trr/...>] (traj.xtc) (Input)
-     Input file description: xtc trr cpt trj gro g96 pdb tng
+     Input file description: xtc trr cpt gro g96 pdb tng
  -mult  [<.xtc/.trr/...> [...]] (traj.xtc) (Input, Opt.)
-     Multiple file description: xtc trr cpt trj gro g96 pdb tng
+     Multiple file description: xtc trr cpt gro g96 pdb tng
  -lib   [<.dat>] (libdata.dat) (Input, Opt., Lib.) Library file description
  -io    [<.dat>] (inout.dat) (In/Out, Opt.) Input/Output file description
  -o     <.xvg>   (Output, Opt.) Output file description
diff --git a/src/gromacs/fileio/confio.c b/src/gromacs/fileio/confio.c
index 36dbc53312..57aff53965 100644
--- a/src/gromacs/fileio/confio.c
+++ b/src/gromacs/fileio/confio.c
@@ -1484,8 +1484,6 @@ void write_sto_conf_indexed(const char *outfile, const char *title,
             gmx_fio_fclose(out);
             break;
         case efTPR:
-        case efTPB:
-        case efTPA:
             gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
             break;
         default:
@@ -1539,8 +1537,6 @@ void write_sto_conf(const char *outfile, const char *title, t_atoms *atoms,
             gmx_fio_fclose(out);
             break;
         case efTPR:
-        case efTPB:
-        case efTPA:
             gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
             break;
         default:
@@ -1612,8 +1608,6 @@ void get_stx_coordnum(const char *infile, int *natoms)
         case efESP:
             *natoms = get_espresso_coordnum(infile);
             break;
-        case efTPA:
-        case efTPB:
         case efTPR:
         {
             t_tpxheader tpx;
@@ -1682,8 +1676,6 @@ void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
             read_espresso_conf(infile, atoms, x, v, box);
             break;
         case efTPR:
-        case efTPB:
-        case efTPA:
             snew(mtop, 1);
             i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
             if (ePBC)
diff --git a/src/gromacs/fileio/filenm.c b/src/gromacs/fileio/filenm.c
index d8b50e526f..bf8212d2c8 100644
--- a/src/gromacs/fileio/filenm.c
+++ b/src/gromacs/fileio/filenm.c
@@ -71,7 +71,7 @@ static const int trxs[] =
 #ifdef USE_XDR
     efXTC, efTRR, efCPT,
 #endif
-    efTRJ, efGRO, efG96, efPDB, efTNG
+    efGRO, efG96, efPDB, efTNG
 };
 #define NTRXS asize(trxs)
 
@@ -89,7 +89,7 @@ static const int tros[] =
 #ifdef USE_XDR
     efXTC, efTRR,
 #endif
-    efTRJ, efGRO, efG96, efPDB, efTNG
+    efGRO, efG96, efPDB, efTNG
 };
 #define NTROS asize(tros)
 
@@ -98,7 +98,7 @@ static const int trns[] =
 #ifdef USE_XDR
     efTRR, efCPT,
 #endif
-    efTRJ, efTNG
+    efTNG
 };
 #define NTRNS asize(trns)
 
@@ -108,29 +108,19 @@ static const int stos[] =
 
 static const int stxs[] =
 {
-    efGRO, efG96, efPDB, efBRK, efENT, efESP,
+    efGRO, efG96, efPDB, efBRK, efENT, efESP
 #ifdef USE_XDR
-    efTPR,
+    , efTPR
 #endif
-    efTPB, efTPA
 };
 #define NSTXS asize(stxs)
 
-static const int tpxs[] =
-{
-#ifdef USE_XDR
-    efTPR,
-#endif
-    efTPB, efTPA
-};
-#define NTPXS asize(tpxs)
-
 static const int tpss[] =
 {
 #ifdef USE_XDR
     efTPR,
 #endif
-    efTPB, efTPA, efGRO, efG96, efPDB, efBRK, efENT
+    efGRO, efG96, efPDB, efBRK, efENT
 };
 #define NTPSS asize(tpss)
 
@@ -155,7 +145,6 @@ static const t_deffile
     { eftGEN, ".???", "traj", NULL,
       "Full precision trajectory", NTRNS, trns },
     { eftXDR, ".trr", "traj", NULL, "Trajectory in portable xdr format" },
-    { eftBIN, ".trj", "traj", NULL, "Trajectory file (architecture specific)" },
     { eftGEN, ".???", "traj_comp", NULL,
       "Compressed trajectory (tng format or portable xdr format)", NTRCOMPRESSED, trcompressed},
     { eftXDR, ".xtc", "traj", NULL,
@@ -179,11 +168,8 @@ static const t_deffile
     { eftASC, ".ndx", "index",  "-n", "Index file", },
     { eftASC, ".top", "topol",  "-p", "Topology file"},
     { eftASC, ".itp", "topinc", NULL, "Include file for topology"},
-    { eftGEN, ".???", "topol", "-s", "Run input file", NTPXS, tpxs },
     { eftGEN, ".???", "topol", "-s", "Structure+mass(db)", NTPSS, tpss },
     { eftXDR, ".tpr", "topol",  "-s", "Portable xdr run input file"},
-    { eftASC, ".tpa", "topol",  "-s", "Ascii run input file"},
-    { eftBIN, ".tpb", "topol",  "-s", "Binary run input file"},
     { eftASC, ".tex", "doc",    "-o", "LaTeX file"},
     { eftASC, ".rtp", "residue", NULL, "Residue Type file used by pdb2gmx" },
     { eftASC, ".atp", "atomtp", NULL, "Atomtype file used by pdb2gmx" },
@@ -231,8 +217,6 @@ const char *ftp2ext_generic(int ftp)
                 return "sto";
             case efSTX:
                 return "stx";
-            case efTPX:
-                return "tpx";
             case efTPS:
                 return "tps";
             default:
diff --git a/src/gromacs/fileio/filenm.h b/src/gromacs/fileio/filenm.h
index d5c1bd6816..e4dfab80ae 100644
--- a/src/gromacs/fileio/filenm.h
+++ b/src/gromacs/fileio/filenm.h
@@ -48,14 +48,14 @@ extern "C" {
 /* this enum should correspond to the array deffile in gmxlib/filenm.c */
 enum {
     efMDP,
-    efTRX, efTRO, efTRN, efTRR, efTRJ, efCOMPRESSED, efXTC, efTNG,
+    efTRX, efTRO, efTRN, efTRR, efCOMPRESSED, efXTC, efTNG,
     efEDR,
     efSTX, efSTO, efGRO, efG96, efPDB, efBRK, efENT, efESP, efPQR,
     efCPT,
     efLOG, efXVG, efOUT,
     efNDX,
     efTOP, efITP,
-    efTPX, efTPS, efTPR, efTPA, efTPB,
+    efTPS, efTPR,
     efTEX, efRTP, efATP, efHDB,
     efDAT, efDLG,
     efMAP, efEPS, efMAT, efM2P,
diff --git a/src/gromacs/fileio/gmxfio.c b/src/gromacs/fileio/gmxfio.c
index 3a38bf87f3..24dbc9f54a 100644
--- a/src/gromacs/fileio/gmxfio.c
+++ b/src/gromacs/fileio/gmxfio.c
@@ -86,51 +86,20 @@ static tMPI_Thread_mutex_t open_file_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
 static const int ftpXDR[] =
 { efTPR, efTRR, efEDR, efXTC, efTNG, efMTX, efCPT };
 static const int ftpASC[] =
-{ efTPA, efGRO, efPDB };
+{ efGRO, efPDB, efG96 };
 static const int ftpBIN[] =
-{ efTPB, efTRJ, efTNG };
+{ efTNG };
 #ifdef HAVE_XML
 static const int ftpXML[] =
 {   efXML};
 #endif
 
-const char *itemstr[eitemNR] =
-{
-    "[header]", "[inputrec]", "[box]", "[topology]", "[coordinates]",
-    "[velocities]", "[forces]"
-};
-
 const char *eioNames[eioNR] =
 {
     "REAL", "INT", "GMX_STE_T", "UCHAR", "NUCHAR", "USHORT", "RVEC", "NRVEC",
     "IVEC", "STRING"
 };
 
-
-
-/* Comment strings for TPA only */
-const char *comment_str[eitemNR] = {
-    "; The header holds information on the number of atoms etc. and on whether\n"
-    "; certain items are present in the file or not.\n"
-    "; \n"
-    ";                             WARNING\n"
-    ";                   DO NOT EDIT THIS FILE BY HAND\n"
-    "; The GROMACS preprocessor performs a lot of checks on your input that\n"
-    "; you ignore when editing this. Your simulation may crash because of this\n",
-    "; The inputrec holds the parameters for MD such as the number of steps,\n"
-    "; the timestep and the cut-offs.\n",
-    "; The simulation box in nm.\n",
-    "; The topology section describes the topology of the molecules\n"
-    "; i.e. bonds, angles and dihedrals etc. and also holds the force field\n"
-    "; parameters.\n",
-    "; The atomic coordinates in nm\n",
-    "; The atomic velocities in nm/ps\n",
-    "; The forces on the atoms in nm/ps^2\n"
-};
-
-
-
-
 /******************************************************************
  *
  * Internal functions:
@@ -433,41 +402,34 @@ t_fileio *gmx_fio_open(const char *fn, const char *mode)
     gmx_bool  bRead, bReadWrite;
     int       xdrid;
 
-    if (fn2ftp(fn) == efTPA)
+    /* sanitize the mode string */
+    if (strncmp(mode, "r+", 2) == 0)
+    {
+        strcpy(newmode, "r+");
+    }
+    else if (mode[0] == 'r')
+    {
+        strcpy(newmode, "r");
+    }
+    else if (strncmp(mode, "w+", 2) == 0)
+    {
+        strcpy(newmode, "w+");
+    }
+    else if (mode[0] == 'w')
+    {
+        strcpy(newmode, "w");
+    }
+    else if (strncmp(mode, "a+", 2) == 0)
+    {
+        strcpy(newmode, "a+");
+    }
+    else if (mode[0] == 'a')
     {
-        strcpy(newmode, mode);
+        strcpy(newmode, "a");
     }
     else
     {
-        /* sanitize the mode string */
-        if (strncmp(mode, "r+", 2) == 0)
-        {
-            strcpy(newmode, "r+");
-        }
-        else if (mode[0] == 'r')
-        {
-            strcpy(newmode, "r");
-        }
-        else if (strncmp(mode, "w+", 2) == 0)
-        {
-            strcpy(newmode, "w+");
-        }
-        else if (mode[0] == 'w')
-        {
-            strcpy(newmode, "w");
-        }
-        else if (strncmp(mode, "a+", 2) == 0)
-        {
-            strcpy(newmode, "a+");
-        }
-        else if (mode[0] == 'a')
-        {
-            strcpy(newmode, "a");
-        }
-        else
-        {
-            gmx_fatal(FARGS, "DEATH HORROR in gmx_fio_open, mode is '%s'", mode);
-        }
+        gmx_fatal(FARGS, "DEATH HORROR in gmx_fio_open, mode is '%s'", mode);
     }
 
     /* Check if it should be opened as a binary file */
@@ -546,14 +508,6 @@ t_fileio *gmx_fio_open(const char *fn, const char *mode)
             gmx_fseek(fio->fp, 0, SEEK_END);
         }
     }
-    else
-    {
-        /* Use stdin/stdout for I/O */
-        fio->iFTP   = efTPA;
-        fio->fp     = bRead ? stdin : stdout;
-        fio->fn     = gmx_strdup("STDIO");
-        fio->bStdio = TRUE;
-    }
     fio->bRead             = bRead;
     fio->bReadWrite        = bReadWrite;
     fio->bDouble           = (sizeof(real) == sizeof(double));
diff --git a/src/gromacs/fileio/gmxfio.h b/src/gromacs/fileio/gmxfio.h
index 076d0c3341..8f6401da23 100644
--- a/src/gromacs/fileio/gmxfio.h
+++ b/src/gromacs/fileio/gmxfio.h
@@ -66,9 +66,6 @@ enum {
 
 typedef struct t_fileio t_fileio;
 
-extern const char *itemstr[eitemNR];
-extern const char *comment_str[eitemNR];
-
 /* NOTE ABOUT THREAD SAFETY:
 
    The functions are all thread-safe, provided that two threads don't
@@ -83,11 +80,6 @@ extern const char *comment_str[eitemNR];
 t_fileio *gmx_fio_open(const char *fn, const char *mode);
 /* Open a new file for reading or writing.
  * The file type will be deduced from the file name.
- * If fn is NULL, stdin / stdout will be used for Ascii I/O (TPA type)
- * mode may be "r", "w", or "a". You should append a "b" to the mode
- * if you are writing a binary file, but the routine will also
- * doublecheck it and try to do it if you forgot. This has no effect on
- * unix, but is important on windows.
  */
 
 int gmx_fio_close(t_fileio *fp);
@@ -150,7 +142,7 @@ void gmx_fio_checktype(t_fileio *fio);
  ***************************************************/
 
 void gmx_fio_rewind(t_fileio *fio);
-/* Rewind the tpa file in fio */
+/* Rewind the file in fio */
 
 int gmx_fio_flush(t_fileio *fio);
 /* Flush the fio, returns 0 on success */
diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.c
index 5d0c85380a..db684d3699 100644
--- a/src/gromacs/fileio/tpxio.c
+++ b/src/gromacs/fileio/tpxio.c
@@ -225,50 +225,6 @@ static const t_ftupd ftupd[] = {
 /* Needed for backward compatibility */
 #define MAXNODES 256
 
-static void _do_section(t_fileio *fio, int key, gmx_bool bRead, const char *src,
-                        int line)
-{
-    char     buf[STRLEN];
-    gmx_bool bDbg;
-
-    if (gmx_fio_getftp(fio) == efTPA)
-    {
-        if (!bRead)
-        {
-            gmx_fio_write_string(fio, itemstr[key]);
-            bDbg       = gmx_fio_getdebug(fio);
-            gmx_fio_setdebug(fio, FALSE);
-            gmx_fio_write_string(fio, comment_str[key]);
-            gmx_fio_setdebug(fio, bDbg);
-        }
-        else
-        {
-            if (gmx_fio_getdebug(fio))
-            {
-                fprintf(stderr, "Looking for section %s (%s, %d)",
-                        itemstr[key], src, line);
-            }
-
-            do
-            {
-                gmx_fio_do_string(fio, buf);
-            }
-            while ((gmx_strcasecmp(buf, itemstr[key]) != 0));
-
-            if (gmx_strcasecmp(buf, itemstr[key]) != 0)
-            {
-                gmx_fatal(FARGS, "\nCould not find section heading %s", itemstr[key]);
-            }
-            else if (gmx_fio_getdebug(fio))
-            {
-                fprintf(stderr, " and found it\n");
-            }
-        }
-    }
-}
-
-#define do_section(fio, key, bRead) _do_section(fio, key, bRead, __FILE__, __LINE__)
-
 /**************************************************************
  *
  * Now the higer level routines that do io of the structures and arrays
@@ -3200,7 +3156,7 @@ static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
     gmx_fio_checktype(fio);
     gmx_fio_setdebug(fio, bDebugMode());
 
-    /* NEW! XDR tpb file */
+    /* XDR binary topology file */
     precision = sizeof(real);
     if (bRead)
     {
@@ -3305,7 +3261,6 @@ static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
                   gmx_fio_getname(fio), fver, tpx_version);
     }
 
-    do_section(fio, eitemHEADER, bRead);
     gmx_fio_do_int(fio, tpx->natoms);
     if (fver >= 28)
     {
@@ -3400,7 +3355,6 @@ static int do_tpx(t_fileio *fio, gmx_bool bRead,
 #define do_test(fio, b, p) if (bRead && (p != NULL) && !b) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
 
     do_test(fio, tpx.bBox, state->box);
-    do_section(fio, eitemBOX, bRead);
     if (tpx.bBox)
     {
         gmx_fio_ndo_rvec(fio, state->box, DIM);
@@ -3447,7 +3401,6 @@ static int do_tpx(t_fileio *fio, gmx_bool bRead,
     if (file_version < 26)
     {
         do_test(fio, tpx.bIr, ir);
-        do_section(fio, eitemIR, bRead);
         if (tpx.bIr)
         {
             if (ir)
@@ -3474,7 +3427,6 @@ static int do_tpx(t_fileio *fio, gmx_bool bRead,
     }
 
     do_test(fio, tpx.bTop, mtop);
-    do_section(fio, eitemTOP, bRead);
     if (tpx.bTop)
     {
         if (mtop)
@@ -3488,7 +3440,6 @@ static int do_tpx(t_fileio *fio, gmx_bool bRead,
         }
     }
     do_test(fio, tpx.bX, state->x);
-    do_section(fio, eitemX, bRead);
     if (tpx.bX)
     {
         if (bRead)
@@ -3499,7 +3450,6 @@ static int do_tpx(t_fileio *fio, gmx_bool bRead,
     }
 
     do_test(fio, tpx.bV, state->v);
-    do_section(fio, eitemV, bRead);
     if (tpx.bV)
     {
         if (bRead)
@@ -3510,7 +3460,6 @@ static int do_tpx(t_fileio *fio, gmx_bool bRead,
     }
 
     do_test(fio, tpx.bF, f);
-    do_section(fio, eitemF, bRead);
     if (tpx.bF)
     {
         gmx_fio_ndo_rvec(fio, f, state->natoms);
@@ -3528,7 +3477,6 @@ static int do_tpx(t_fileio *fio, gmx_bool bRead,
     if (file_version >= 26)
     {
         do_test(fio, tpx.bIr, ir);
-        do_section(fio, eitemIR, bRead);
         if (tpx.bIr)
         {
             if (file_version >= 53)
@@ -3712,15 +3660,7 @@ int read_tpx_top(const char *fn,
 
 gmx_bool fn2bTPX(const char *file)
 {
-    switch (fn2ftp(file))
-    {
-        case efTPR:
-        case efTPB:
-        case efTPA:
-            return TRUE;
-        default:
-            return FALSE;
-    }
+    return (efTPR == fn2ftp(file));
 }
 
 static void done_gmx_groups_t(gmx_groups_t *g)
diff --git a/src/gromacs/fileio/tpxio.h b/src/gromacs/fileio/tpxio.h
index 3611be60d2..433742fdcd 100644
--- a/src/gromacs/fileio/tpxio.h
+++ b/src/gromacs/fileio/tpxio.h
@@ -85,10 +85,7 @@ typedef struct
  * These routines handle reading and writing of preprocessed
  * topology files in any of the following formats:
  * TPR : topology in XDR format, portable accross platforms
- * TPB : binary topology, not portable accross platforms
- * TPA : ascii topology (possibbly huge)
  * TRR : trajectory in XDR format (non compressed)
- * TRJ : trajectory in binary format
  *
  * Files are written in the precision with which the source are compiled,
  * but double and single precision can be read by either.
@@ -115,8 +112,6 @@ void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
 void write_tpx_state(const char *fn,
                      t_inputrec *ir, t_state *state, struct gmx_mtop_t *mtop);
 /* Write a file, and close it again.
- * If fn == NULL, an efTPA file will be written to stdout (which
- * will not be closed afterwards)
  */
 
 void read_tpx_state(const char *fn,
@@ -126,8 +121,6 @@ int read_tpx(const char *fn,
              t_inputrec *ir, matrix box, int *natoms,
              rvec *x, rvec *v, rvec *f, struct gmx_mtop_t *mtop);
 /* Read a file, and close it again.
- * If fn == NULL, an efTPA file will be read from stdin (which
- * will not be closed afterwards)
  * When step, t or lambda are NULL they will not be stored.
  * Returns ir->ePBC, if it could be read from the file.
  */
diff --git a/src/gromacs/fileio/trnio.h b/src/gromacs/fileio/trnio.h
index 8fd25d14d0..59bf1d4122 100644
--- a/src/gromacs/fileio/trnio.h
+++ b/src/gromacs/fileio/trnio.h
@@ -40,8 +40,8 @@
 
 /**************************************************************
  *
- * These routines handle trj (trajectory) I/O, they read and
- * write trj/trr files. The routines should be able to read single
+ * These routines handle trr (trajectory) I/O, they read and
+ * write trr files. The routines should be able to read single
  * and double precision files without the user noting it.
  * The files are backward compatible, therefore the header holds
  * some unused variables.
@@ -83,7 +83,7 @@ typedef struct           /* This struct describes the order and the	*/
 } t_trnheader;
 
 t_fileio *open_trn(const char *fn, const char *mode);
-/* Open a trj / trr file */
+/* Open a trr / trr file */
 
 void close_trn(t_fileio *fio);
 /* Close it */
diff --git a/src/gromacs/fileio/trxio.c b/src/gromacs/fileio/trxio.c
index b515578ef3..0f39b6c46b 100644
--- a/src/gromacs/fileio/trxio.c
+++ b/src/gromacs/fileio/trxio.c
@@ -338,7 +338,6 @@ int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
 
     switch (ftp)
     {
-        case efTRJ:
         case efTRR:
         case efTNG:
             break;
@@ -353,7 +352,6 @@ int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
 
     switch (ftp)
     {
-        case efTRJ:
         case efTRR:
         case efTNG:
             if (fr->bV)
@@ -395,7 +393,6 @@ int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
         case efXTC:
             write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
             break;
-        case efTRJ:
         case efTRR:
             fwrite_trn(status->fio, nframes_read(status),
                        fr->time, fr->step, fr->box, nind, xout, vout, fout);
@@ -433,8 +430,6 @@ int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
 
     switch (ftp)
     {
-        case efTRN:
-        case efTRJ:
         case efTRR:
         case efTNG:
             if (vout)
@@ -534,7 +529,6 @@ int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc)
 
     switch (gmx_fio_getftp(status->fio))
     {
-        case efTRJ:
         case efTRR:
             break;
         default:
@@ -551,7 +545,6 @@ int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc)
         case efXTC:
             write_xtc(status->fio, fr->natoms, fr->step, fr->time, fr->box, fr->x, prec);
             break;
-        case efTRJ:
         case efTRR:
             fwrite_trn(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
                        fr->bX ? fr->x : NULL, fr->bV ? fr->v : NULL, fr->bF ? fr->f : NULL);
@@ -814,7 +807,6 @@ gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status, t_trxfram
         }
         switch (ftp)
         {
-            case efTRJ:
             case efTRR:
                 bRet = gmx_next_frame(status, fr);
                 break;
@@ -948,7 +940,6 @@ int read_first_frame(const output_env_t oenv, t_trxstatus **status,
     }
     switch (ftp)
     {
-        case efTRJ:
         case efTRR:
             break;
         case efCPT:
diff --git a/src/gromacs/fileio/trxio.h b/src/gromacs/fileio/trxio.h
index dab739a34a..f66b4c37f1 100644
--- a/src/gromacs/fileio/trxio.h
+++ b/src/gromacs/fileio/trxio.h
@@ -138,7 +138,7 @@ void write_tng_frame(t_trxstatus        *status,
                      struct t_trxframe  *fr);
 
 void close_trx(t_trxstatus *status);
-/* Close trj file as opened with read_first_x, read_frist_frame
+/* Close trajectory file as opened with read_first_x, read_frist_frame
  * or open_trx. Identical to close_trj.
  */
 
@@ -234,12 +234,12 @@ gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t, rvec
  */
 
 void close_trj(t_trxstatus *status);
-/* Close trj file as opened with read_first_x, read_frist_frame
+/* Close trajectory file as opened with read_first_x, read_first_frame
  * or open_trx. Identical to close_trx.
  */
 
 void rewind_trj(t_trxstatus *status);
-/* Rewind trj file as opened with read_first_x */
+/* Rewind trajectory file as opened with read_first_x */
 
 struct t_topology *read_top(const char *fn, int *ePBC);
 /* Extract a topology data structure from a topology file.
diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index 4282430de0..43a3180d67 100644
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -671,7 +671,7 @@ int gmx_density(int argc, char *argv[])
     t_filenm           fnm[] = { /* files for g_density       */
         { efTRX, "-f", NULL,  ffREAD },
         { efNDX, NULL, NULL,  ffOPTRD },
-        { efTPX, NULL, NULL,  ffREAD },
+        { efTPR, NULL, NULL,  ffREAD },
         { efDAT, "-ei", "electrons", ffOPTRD }, /* file with nr. of electrons */
         { efXVG, "-o", "density", ffWRITE },
     };
@@ -693,7 +693,7 @@ int gmx_density(int argc, char *argv[])
     /* Calculate axis */
     axis = toupper(axtitle[0]) - 'X';
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
     if (dens_opt[0][0] == 'n')
     {
         for (i = 0; (i < top->atoms.nr); i++)
diff --git a/src/gromacs/gmxana/gmx_densorder.cpp b/src/gromacs/gmxana/gmx_densorder.cpp
index 79c9e68a11..5d8a8d9bb1 100644
--- a/src/gromacs/gmxana/gmx_densorder.cpp
+++ b/src/gromacs/gmxana/gmx_densorder.cpp
@@ -726,7 +726,7 @@ int gmx_densorder(int argc, char *argv[])
 
 
     t_filenm fnm[] = {
-        { efTPX, "-s",  NULL, ffREAD },               /* this is for the topology */
+        { efTPR, "-s",  NULL, ffREAD },               /* this is for the topology */
         { efTRX, "-f", NULL, ffREAD },                /* and this for the trajectory */
         { efNDX, "-n", NULL, ffREAD},                 /* this is to select groups */
         { efDAT, "-o", "Density4D", ffOPTWR},         /* This is for outputting the entire 4D densityfield in binary format */
@@ -751,7 +751,7 @@ int gmx_densorder(int argc, char *argv[])
     bRawOut  = opt2bSet("-or", NFILE, fnm);
     bGraph   = opt2bSet("-og", NFILE, fnm);
     bOut     = opt2bSet("-o", NFILE, fnm);
-    top      = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+    top      = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
     snew(grpname, 1);
     snew(index, 1);
     snew(ngx, 1);
diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index 569954d341..68e338fe04 100644
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -1590,7 +1590,7 @@ int gmx_dipoles(int argc, char *argv[])
     t_filenm       fnm[] = {
         { efEDR, "-en", NULL,         ffOPTRD },
         { efTRX, "-f", NULL,           ffREAD },
-        { efTPX, NULL, NULL,           ffREAD },
+        { efTPR, NULL, NULL,           ffREAD },
         { efNDX, NULL, NULL,           ffOPTRD },
         { efXVG, "-o",   "Mtot",       ffWRITE },
         { efXVG, "-eps", "epsilon",    ffWRITE },
@@ -1664,7 +1664,7 @@ int gmx_dipoles(int argc, char *argv[])
     }
 
     snew(top, 1);
-    ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm), NULL, box,
+    ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm), NULL, box,
                         &natoms, NULL, NULL, NULL, top);
 
     snew(gnx, ncos);
diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index 4852d3616b..d7e1dd8af8 100644
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -717,7 +717,7 @@ int gmx_disre(int argc, char *argv[])
     gmx_rmpbc_t     gpbc = NULL;
 
     t_filenm        fnm[] = {
-        { efTPX, NULL, NULL, ffREAD },
+        { efTPR, NULL, NULL, ffREAD },
         { efTRX, "-f", NULL, ffREAD },
         { efXVG, "-ds", "drsum",  ffWRITE },
         { efXVG, "-da", "draver", ffWRITE },
@@ -745,9 +745,9 @@ int gmx_disre(int argc, char *argv[])
         init5(ntop);
     }
 
-    read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &header, FALSE, NULL, NULL);
+    read_tpxheader(ftp2fn(efTPR, NFILE, fnm), &header, FALSE, NULL, NULL);
     snew(xtop, header.natoms);
-    read_tpx(ftp2fn(efTPX, NFILE, fnm), &ir, box, &ntopatoms, xtop, NULL, NULL, &mtop);
+    read_tpx(ftp2fn(efTPR, NFILE, fnm), &ir, box, &ntopatoms, xtop, NULL, NULL, &mtop);
     bPDB = opt2bSet("-q", NFILE, fnm);
     if (bPDB)
     {
diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index e353d7a3e8..07439151bc 100644
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -305,7 +305,7 @@ int gmx_dos(int argc, char *argv[])
 
     t_filenm            fnm[] = {
         { efTRN, "-f",    NULL,    ffREAD  },
-        { efTPX, "-s",    NULL,    ffREAD  },
+        { efTPR, "-s",    NULL,    ffREAD  },
         { efNDX, NULL,    NULL,    ffOPTRD },
         { efXVG, "-vacf", "vacf",  ffWRITE },
         { efXVG, "-mvacf", "mvacf", ffWRITE },
@@ -342,7 +342,7 @@ int gmx_dos(int argc, char *argv[])
     please_cite(fplog, "Pascal2011a");
     please_cite(fplog, "Caleman2011b");
 
-    read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
+    read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
                   TRUE);
     V     = det(box);
     tmass = 0;
diff --git a/src/gromacs/gmxana/gmx_editconf.c b/src/gromacs/gmxana/gmx_editconf.c
index c710ecfd15..abe79cb071 100644
--- a/src/gromacs/gmxana/gmx_editconf.c
+++ b/src/gromacs/gmxana/gmx_editconf.c
@@ -793,11 +793,9 @@ int gmx_editconf(int argc, char *argv[])
         gmx_fatal(FARGS, "Output file should be a .pdb file"
                   " when using the -grasp option\n");
     }
-    if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
-                               (fn2ftp(infile) == efTPA) ||
-                               (fn2ftp(infile) == efTPB)))
+    if ((bMead || bGrasp) && (fn2ftp(infile) != efTPR))
     {
-        gmx_fatal(FARGS, "Input file should be a .tp[abr] file"
+        gmx_fatal(FARGS, "Input file should be a .tpr file"
                   " when using the -mead option\n");
     }
 
diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index cc3958fda1..96a153cf0c 100644
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -2027,7 +2027,7 @@ int gmx_energy(int argc, char *argv[])
     t_filenm           fnm[] = {
         { efEDR, "-f",    NULL,      ffREAD  },
         { efEDR, "-f2",   NULL,      ffOPTRD },
-        { efTPX, "-s",    NULL,      ffOPTRD },
+        { efTPR, "-s",    NULL,      ffOPTRD },
         { efXVG, "-o",    "energy",  ffWRITE },
         { efXVG, "-viol", "violaver", ffOPTWR },
         { efXVG, "-pairs", "pairs",   ffOPTWR },
@@ -2172,7 +2172,7 @@ int gmx_energy(int argc, char *argv[])
 
         if (bORIRE || bOTEN)
         {
-            get_orires_parms(ftp2fn(efTPX, NFILE, fnm), &nor, &nex, &or_label, &oobs);
+            get_orires_parms(ftp2fn(efTPR, NFILE, fnm), &nor, &nex, &or_label, &oobs);
         }
 
         if (bORIRE)
@@ -2297,7 +2297,7 @@ int gmx_energy(int argc, char *argv[])
     }
     else if (bDisRe)
     {
-        nbounds = get_bounds(ftp2fn(efTPX, NFILE, fnm), &bounds, &index, &pair, &npairs,
+        nbounds = get_bounds(ftp2fn(efTPR, NFILE, fnm), &bounds, &index, &pair, &npairs,
                              &mtop, &top, &ir);
         snew(violaver, npairs);
         out = xvgropen(opt2fn("-o", NFILE, fnm), "Sum of Violations",
@@ -2316,7 +2316,7 @@ int gmx_energy(int argc, char *argv[])
     }
     else if (bDHDL)
     {
-        get_dhdl_parms(ftp2fn(efTPX, NFILE, fnm), &ir);
+        get_dhdl_parms(ftp2fn(efTPR, NFILE, fnm), &ir);
     }
 
     /* Initiate energies and set them to zero */
diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index fc1ac0e8e8..1301d8e01a 100644
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -395,7 +395,7 @@ int gmx_genion(int argc, char *argv[])
     output_env_t       oenv;
     gmx_rng_t          rng;
     t_filenm           fnm[] = {
-        { efTPX, NULL,  NULL,      ffREAD  },
+        { efTPR, NULL,  NULL,      ffREAD  },
         { efNDX, NULL,  NULL,      ffOPTRD },
         { efSTO, "-o",  NULL,      ffWRITE },
         { efTOP, "-p",  "topol",   ffOPTRW }
@@ -420,7 +420,7 @@ int gmx_genion(int argc, char *argv[])
     }
 
     /* Read atom positions and charges */
-    read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, &x, &v, box, FALSE);
+    read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, &x, &v, box, FALSE);
     atoms = top.atoms;
 
     /* Compute total charge */
diff --git a/src/gromacs/gmxana/gmx_h2order.c b/src/gromacs/gmxana/gmx_h2order.c
index 314f20c46a..27e918b8d3 100644
--- a/src/gromacs/gmxana/gmx_h2order.c
+++ b/src/gromacs/gmxana/gmx_h2order.c
@@ -304,7 +304,7 @@ int gmx_h2order(int argc, char *argv[])
         { efTRX, "-f", NULL,  ffREAD },     /* trajectory file            */
         { efNDX, NULL, NULL,  ffREAD },     /* index file         */
         { efNDX, "-nm", NULL, ffOPTRD },    /* index with micelle atoms   */
-        { efTPX, NULL, NULL,  ffREAD },     /* topology file              */
+        { efTPR, NULL, NULL,  ffREAD },     /* topology file              */
         { efXVG, "-o",  "order", ffWRITE }, /* xvgr output file       */
     };
 
@@ -318,7 +318,7 @@ int gmx_h2order(int argc, char *argv[])
     }
     bMicel = opt2bSet("-nm", NFILE, fnm);
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
 
     rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &ngx, &index, &grpname);
 
diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index 53fe4fac9a..c226bed5bf 100644
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -3637,7 +3637,7 @@ int gmx_hbond(int argc, char *argv[])
     };
     t_filenm    fnm[] = {
         { efTRX, "-f",   NULL,     ffREAD  },
-        { efTPX, NULL,   NULL,     ffREAD  },
+        { efTPR, NULL,   NULL,     ffREAD  },
         { efNDX, NULL,   NULL,     ffOPTRD },
         /*    { efNDX, "-sel", "select", ffOPTRD },*/
         { efXVG, "-num", "hbnum",  ffWRITE },
@@ -3822,7 +3822,7 @@ int gmx_hbond(int argc, char *argv[])
     hb = mk_hbdata(bHBmap, opt2bSet("-dan", NFILE, fnm), bMerge || bContact, bGem, gemmode);
 
     /* get topology */
-    read_tpx_top(ftp2fn(efTPX, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
+    read_tpx_top(ftp2fn(efTPR, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
 
     snew(grpnames, grNR);
     snew(index, grNR);
diff --git a/src/gromacs/gmxana/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
index 70c24752fb..b1bbcb8d6d 100644
--- a/src/gromacs/gmxana/gmx_helix.c
+++ b/src/gromacs/gmxana/gmx_helix.c
@@ -157,7 +157,7 @@ int gmx_helix(int argc, char *argv[])
     gmx_rmpbc_t    gpbc = NULL;
     gmx_bool       bRange;
     t_filenm       fnm[] = {
-        { efTPX, NULL,  NULL,   ffREAD  },
+        { efTPR, NULL,  NULL,   ffREAD  },
         { efNDX, NULL,  NULL,   ffREAD  },
         { efTRX, "-f",  NULL,   ffREAD  },
         { efSTO, "-cz", "zconf", ffWRITE },
@@ -173,7 +173,7 @@ int gmx_helix(int argc, char *argv[])
     bRange = (opt2parg_bSet("-ahxstart", asize(pa), pa) &&
               opt2parg_bSet("-ahxend", asize(pa), pa));
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
 
     natoms = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
 
@@ -208,7 +208,7 @@ int gmx_helix(int argc, char *argv[])
 
     /* Read reference frame from tpx file to compute helix length */
     snew(xref, top->atoms.nr);
-    read_tpx(ftp2fn(efTPX, NFILE, fnm),
+    read_tpx(ftp2fn(efTPR, NFILE, fnm),
              NULL, NULL, &natoms, xref, NULL, NULL, NULL);
     calc_hxprops(nres, bb, xref);
     do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, bRange, rStart, rEnd);
diff --git a/src/gromacs/gmxana/gmx_helixorient.c b/src/gromacs/gmxana/gmx_helixorient.c
index b42a518b1d..dfd3a1f7cf 100644
--- a/src/gromacs/gmxana/gmx_helixorient.c
+++ b/src/gromacs/gmxana/gmx_helixorient.c
@@ -149,7 +149,7 @@ int gmx_helixorient(int argc, char *argv[])
 #define NPA asize(pa)
 
     t_filenm fnm[] = {
-        { efTPX, NULL, NULL, ffREAD },
+        { efTPR, NULL, NULL, ffREAD },
         { efTRX, "-f", NULL, ffREAD },
         { efNDX, NULL, NULL, ffOPTRD },
         { efDAT, "-oaxis",    "helixaxis", ffWRITE },
@@ -169,7 +169,7 @@ int gmx_helixorient(int argc, char *argv[])
         return 0;
     }
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
 
     for (i = 0; i < 3; i++)
     {
diff --git a/src/gromacs/gmxana/gmx_hydorder.c b/src/gromacs/gmxana/gmx_hydorder.c
index af7ecb739e..74de61fc81 100644
--- a/src/gromacs/gmxana/gmx_hydorder.c
+++ b/src/gromacs/gmxana/gmx_hydorder.c
@@ -628,7 +628,7 @@ int gmx_hydorder(int argc, char *argv[])
     t_filenm           fnm[] = {                      /* files for g_order    */
         { efTRX, "-f", NULL,  ffREAD },               /* trajectory file              */
         { efNDX, "-n", NULL,  ffREAD },               /* index file           */
-        { efTPX, "-s", NULL,  ffREAD },               /* topology file                */
+        { efTPR, "-s", NULL,  ffREAD },               /* topology file                */
         { efXPM, "-o", "intf",  ffWRMULT},            /* XPM- surface maps	*/
         { efOUT, "-or", "raw", ffOPTWRMULT },         /* xvgr output file           */
         { efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* Fourier spectrum interfaces */
@@ -655,7 +655,7 @@ int gmx_hydorder(int argc, char *argv[])
     }
 
     ndxfnm = ftp2fn(efNDX, NFILE, fnm);
-    tpsfnm = ftp2fn(efTPX, NFILE, fnm);
+    tpsfnm = ftp2fn(efTPR, NFILE, fnm);
     trxfnm = ftp2fn(efTRX, NFILE, fnm);
 
     /* Calculate axis */
diff --git a/src/gromacs/gmxana/gmx_mk_angndx.c b/src/gromacs/gmxana/gmx_mk_angndx.c
index 1b1ceeead6..d27546891a 100644
--- a/src/gromacs/gmxana/gmx_mk_angndx.c
+++ b/src/gromacs/gmxana/gmx_mk_angndx.c
@@ -272,7 +272,7 @@ int gmx_mk_angndx(int argc, char *argv[])
     int               *nr;
     char             **grpnames;
     t_filenm           fnm[] = {
-        { efTPX, NULL, NULL, ffREAD  },
+        { efTPR, NULL, NULL, ffREAD  },
         { efNDX, NULL, "angle", ffWRITE }
     };
 #define NFILE asize(fnm)
@@ -286,7 +286,7 @@ int gmx_mk_angndx(int argc, char *argv[])
 
     ft = select_ftype(opt[0], &nft, &mult);
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), NULL);
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), NULL);
 
     ntype = calc_ntype(nft, ft, &(top->idef));
     snew(grpnames, ntype);
diff --git a/src/gromacs/gmxana/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
index 63fb24daa3..519f44a3bf 100644
--- a/src/gromacs/gmxana/gmx_nmeig.c
+++ b/src/gromacs/gmxana/gmx_nmeig.c
@@ -344,7 +344,7 @@ int gmx_nmeig(int argc, char *argv[])
 
     t_filenm               fnm[] = {
         { efMTX, "-f", "hessian",    ffREAD  },
-        { efTPX, NULL, NULL,         ffREAD  },
+        { efTPR, NULL, NULL,         ffREAD  },
         { efXVG, "-of", "eigenfreq", ffWRITE },
         { efXVG, "-ol", "eigenval",  ffWRITE },
         { efXVG, "-os", "spectrum",  ffOPTWR },
@@ -360,10 +360,10 @@ int gmx_nmeig(int argc, char *argv[])
     }
 
     /* Read tpr file for volume and number of harmonic terms */
-    read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &tpx, TRUE, &version, &generation);
+    read_tpxheader(ftp2fn(efTPR, NFILE, fnm), &tpx, TRUE, &version, &generation);
     snew(top_x, tpx.natoms);
 
-    read_tpx(ftp2fn(efTPX, NFILE, fnm), NULL, box, &natoms,
+    read_tpx(ftp2fn(efTPR, NFILE, fnm), NULL, box, &natoms,
              top_x, NULL, NULL, &mtop);
     if (bCons)
     {
diff --git a/src/gromacs/gmxana/gmx_options.c b/src/gromacs/gmxana/gmx_options.c
index 4a98b8348a..addcdc5f4b 100644
--- a/src/gromacs/gmxana/gmx_options.c
+++ b/src/gromacs/gmxana/gmx_options.c
@@ -85,7 +85,7 @@ gmx_options(int argc, char *argv[])
 
         "All GROMACS programs can read compressed or g-zipped files. There "
         "might be a problem with reading compressed [TT].xtc[tt], "
-        "[TT].trr[tt] and [TT].trj[tt] files, but these will not compress "
+        "[TT].trr[tt] files, but these will not compress "
         "very well anyway.",
 
         "Most GROMACS programs can process a trajectory with fewer atoms than "
diff --git a/src/gromacs/gmxana/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
index 0c6e723316..7c2b600d05 100644
--- a/src/gromacs/gmxana/gmx_order.c
+++ b/src/gromacs/gmxana/gmx_order.c
@@ -961,7 +961,7 @@ int gmx_order(int argc, char *argv[])
         { efTRX, "-f", NULL,  ffREAD },               /* trajectory file              */
         { efNDX, "-n", NULL,  ffREAD },               /* index file           */
         { efNDX, "-nr", NULL,  ffREAD },              /* index for radial axis calculation	  */
-        { efTPX, NULL, NULL,  ffREAD },               /* topology file                */
+        { efTPR, NULL, NULL,  ffREAD },               /* topology file                */
         { efXVG, "-o", "order", ffWRITE },            /* xvgr output file     */
         { efXVG, "-od", "deuter", ffWRITE },          /* xvgr output file           */
         { efPDB, "-ob", NULL, ffWRITE },              /* write Scd as B factors to PDB if permolecule           */
@@ -989,7 +989,7 @@ int gmx_order(int argc, char *argv[])
     sgfnm  = opt2fn_null("-Sg", NFILE, fnm);
     skfnm  = opt2fn_null("-Sk", NFILE, fnm);
     ndxfnm = opt2fn_null("-n", NFILE, fnm);
-    tpsfnm = ftp2fn(efTPX, NFILE, fnm);
+    tpsfnm = ftp2fn(efTPR, NFILE, fnm);
     trxfnm = ftp2fn(efTRX, NFILE, fnm);
 
     /* Calculate axis */
@@ -1060,7 +1060,7 @@ int gmx_order(int argc, char *argv[])
             fprintf(stderr, "Taking carbons as unsaturated!\n");
         }
 
-        top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+        top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
 
         block = init_index(ftp2fn(efNDX, NFILE, fnm), &grpname);
         index = block->index;                   /* get indices from t_block block */
diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index b132b6b2b1..0dc23d9f85 100644
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -1106,9 +1106,9 @@ int gmx_pme_error(int argc, char *argv[])
 
 
     static t_filenm fnm[] = {
-        { efTPX, "-s",     NULL,    ffREAD },
+        { efTPR, "-s",     NULL,    ffREAD },
         { efOUT, "-o",    "error",  ffWRITE },
-        { efTPX, "-so",   "tuned",  ffOPTWR }
+        { efTPR, "-so",   "tuned",  ffOPTWR }
     };
 
     output_env_t    oenv = NULL;
diff --git a/src/gromacs/gmxana/gmx_polystat.c b/src/gromacs/gmxana/gmx_polystat.c
index b98fdaf12a..367c1c5ff6 100644
--- a/src/gromacs/gmxana/gmx_polystat.c
+++ b/src/gromacs/gmxana/gmx_polystat.c
@@ -139,7 +139,7 @@ int gmx_polystat(int argc, char *argv[])
     };
 
     t_filenm        fnm[] = {
-        { efTPX, NULL, NULL,  ffREAD  },
+        { efTPR, NULL, NULL,  ffREAD  },
         { efTRX, "-f", NULL,  ffREAD  },
         { efNDX, NULL, NULL,  ffOPTRD },
         { efXVG, "-o", "polystat",  ffWRITE },
@@ -184,7 +184,7 @@ int gmx_polystat(int argc, char *argv[])
     }
 
     snew(top, 1);
-    ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm),
+    ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm),
                         NULL, box, &natoms, NULL, NULL, NULL, top);
 
     fprintf(stderr, "Select a group of polymer mainchain atoms:\n");
diff --git a/src/gromacs/gmxana/gmx_potential.c b/src/gromacs/gmxana/gmx_potential.c
index 54ddc2ac8a..ba223b01cc 100644
--- a/src/gromacs/gmxana/gmx_potential.c
+++ b/src/gromacs/gmxana/gmx_potential.c
@@ -459,7 +459,7 @@ int gmx_potential(int argc, char *argv[])
     t_filenm    fnm[] = {                      /* files for g_order       */
         { efTRX, "-f", NULL,  ffREAD },        /* trajectory file             */
         { efNDX, NULL, NULL,  ffREAD },        /* index file          */
-        { efTPX, NULL, NULL,  ffREAD },        /* topology file               */
+        { efTPR, NULL, NULL,  ffREAD },        /* topology file               */
         { efXVG, "-o", "potential", ffWRITE }, /* xvgr output file    */
         { efXVG, "-oc", "charge", ffWRITE },   /* xvgr output file    */
         { efXVG, "-of", "field", ffWRITE },    /* xvgr output file    */
@@ -477,7 +477,7 @@ int gmx_potential(int argc, char *argv[])
     /* Calculate axis */
     axis = toupper(axtitle[0]) - 'X';
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
 
     snew(grpname, ngrps);
     snew(index, ngrps);
diff --git a/src/gromacs/gmxana/gmx_rama.c b/src/gromacs/gmxana/gmx_rama.c
index f5db3dfada..711bac7ece 100644
--- a/src/gromacs/gmxana/gmx_rama.c
+++ b/src/gromacs/gmxana/gmx_rama.c
@@ -80,7 +80,7 @@ int gmx_rama(int argc, char *argv[])
     output_env_t oenv;
     t_filenm     fnm[] = {
         { efTRX, "-f", NULL,  ffREAD },
-        { efTPX, NULL, NULL,  ffREAD },
+        { efTPR, NULL, NULL,  ffREAD },
         { efXVG, NULL, "rama", ffWRITE }
     };
 #define NFILE asize(fnm)
@@ -93,7 +93,7 @@ int gmx_rama(int argc, char *argv[])
 
 
     snew(xr, 1);
-    init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPX, NFILE, fnm), xr, 3);
+    init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPR, NFILE, fnm), xr, 3);
 
     out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Ramachandran Plot", "Phi", "Psi", oenv);
     xvgr_line_props(out, 0, elNone, ecFrank, oenv);
diff --git a/src/gromacs/gmxana/gmx_rotacf.c b/src/gromacs/gmxana/gmx_rotacf.c
index 18f4f33a9d..0895c01bb2 100644
--- a/src/gromacs/gmxana/gmx_rotacf.c
+++ b/src/gromacs/gmxana/gmx_rotacf.c
@@ -100,7 +100,7 @@ int gmx_rotacf(int argc, char *argv[])
     int             ePBC;
     t_filenm        fnm[] = {
         { efTRX, "-f", NULL,  ffREAD  },
-        { efTPX, NULL, NULL,  ffREAD },
+        { efTPR, NULL, NULL,  ffREAD },
         { efNDX, NULL, NULL,  ffREAD  },
         { efXVG, "-o", "rotacf",  ffWRITE }
     };
@@ -141,7 +141,7 @@ int gmx_rotacf(int argc, char *argv[])
                   "these can not be atom doublets\n");
     }
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
 
     snew(c1, nvec);
     for (i = 0; (i < nvec); i++)
diff --git a/src/gromacs/gmxana/gmx_saltbr.c b/src/gromacs/gmxana/gmx_saltbr.c
index 23381e2db7..47b3e6cca7 100644
--- a/src/gromacs/gmxana/gmx_saltbr.c
+++ b/src/gromacs/gmxana/gmx_saltbr.c
@@ -150,7 +150,7 @@ int gmx_saltbr(int argc, char *argv[])
     };
     t_filenm        fnm[] = {
         { efTRX, "-f",  NULL, ffREAD },
-        { efTPX, NULL,  NULL, ffREAD },
+        { efTPR, NULL,  NULL, ffREAD },
     };
 #define NFILE asize(fnm)
 
@@ -190,7 +190,7 @@ int gmx_saltbr(int argc, char *argv[])
         return 0;
     }
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
     cg  = mk_charge(&top->atoms, &(top->cgs), &ncg);
     snew(cgdist, ncg);
     snew(nWithin, ncg);
diff --git a/src/gromacs/gmxana/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
index 6838d272a3..a91af5888b 100644
--- a/src/gromacs/gmxana/gmx_sans.c
+++ b/src/gromacs/gmxana/gmx_sans.c
@@ -146,7 +146,7 @@ int gmx_sans(int argc, char *argv[])
 #define NFILE asize(fnm)
 
     t_filenm   fnm[] = {
-        { efTPX,  "-s",       NULL,       ffREAD },
+        { efTPR,  "-s",       NULL,       ffREAD },
         { efTRX,  "-f",       NULL,       ffREAD },
         { efNDX,  NULL,       NULL,       ffOPTRD },
         { efDAT,  "-d",       "nsfactor", ffOPTRD },
@@ -217,7 +217,7 @@ int gmx_sans(int argc, char *argv[])
 
     /* Try to read files */
     fnDAT = ftp2fn(efDAT, NFILE, fnm);
-    fnTPX = ftp2fn(efTPX, NFILE, fnm);
+    fnTPX = ftp2fn(efTPR, NFILE, fnm);
     fnTRX = ftp2fn(efTRX, NFILE, fnm);
 
     gnsf = gmx_neutronstructurefactors_init(fnDAT);
diff --git a/src/gromacs/gmxana/gmx_spol.c b/src/gromacs/gmxana/gmx_spol.c
index af6ed8cc0d..e715f578c3 100644
--- a/src/gromacs/gmxana/gmx_spol.c
+++ b/src/gromacs/gmxana/gmx_spol.c
@@ -205,7 +205,7 @@ int gmx_spol(int argc, char *argv[])
 
     t_filenm        fnm[] = {
         { efTRX, NULL,  NULL,  ffREAD },
-        { efTPX, NULL,  NULL,  ffREAD },
+        { efTPR, NULL,  NULL,  ffREAD },
         { efNDX, NULL,  NULL,  ffOPTRD },
         { efXVG, NULL,  "scdist",  ffWRITE }
     };
@@ -219,7 +219,7 @@ int gmx_spol(int argc, char *argv[])
 
     snew(top, 1);
     snew(ir, 1);
-    read_tpx_top(ftp2fn(efTPX, NFILE, fnm),
+    read_tpx_top(ftp2fn(efTPR, NFILE, fnm),
                  ir, box, &natoms, NULL, NULL, NULL, top);
 
     /* get index groups */
diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
index a0e38488d7..29e064f74b 100644
--- a/src/gromacs/gmxana/gmx_trjconv.c
+++ b/src/gromacs/gmxana/gmx_trjconv.c
@@ -470,7 +470,7 @@ static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
 
 void check_trn(const char *fn)
 {
-    if ((fn2ftp(fn) != efTRJ)  && (fn2ftp(fn) != efTRR))
+    if (fn2ftp(fn) != efTRR)
     {
         gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
     }
@@ -493,7 +493,7 @@ void do_trunc(const char *fn, real t0)
         gmx_fatal(FARGS, "You forgot to set the truncation time");
     }
 
-    /* Check whether this is a .trj file */
+    /* Check whether this is a .trr file */
     check_trn(fn);
 
     in   = open_trn(fn, "r");
@@ -616,18 +616,18 @@ int gmx_trjconv(int argc, char *argv[])
         "[PAR]",
 
         "The following formats are supported for input and output:",
-        "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt]",
+        "[TT].xtc[tt], [TT].trr[tt], [TT].gro[tt], [TT].g96[tt]",
         "and [TT].pdb[tt].",
         "The file formats are detected from the file extension.",
         "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
         "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
         "and from the [TT]-ndec[tt] option for other input formats. The precision",
         "is always taken from [TT]-ndec[tt], when this option is set.",
-        "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
+        "All other formats have fixed precision. [TT].trr[tt]",
         "output can be single or double precision, depending on the precision",
         "of the [THISMODULE] binary.",
         "Note that velocities are only supported in",
-        "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
+        "[TT].trr[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
 
         "Option [TT]-sep[tt] can be used to write every frame to a separate",
         "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
@@ -715,7 +715,7 @@ int gmx_trjconv(int argc, char *argv[])
         "can reduce the number of frames while using low-pass frequency",
         "filtering, this reduces aliasing of high frequency motions.[PAR]",
 
-        "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trj[tt] in place, i.e.",
+        "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trr[tt] in place, i.e.",
         "without copying the file. This is useful when a run has crashed",
         "during disk I/O (i.e. full disk), or when two contiguous",
         "trajectories must be concatenated without having double frames.[PAR]",
@@ -1033,9 +1033,9 @@ int gmx_trjconv(int argc, char *argv[])
         {
             /* check if velocities are possible in input and output files */
             ftpin = fn2ftp(in_file);
-            bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO ||
+            bVels = (ftp == efTRR || ftp == efGRO ||
                      ftp == efG96 || ftp == efTNG)
-                && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO ||
+                && (ftpin == efTRR || ftpin == efGRO ||
                     ftpin == efG96 || ftpin == efTNG || ftpin == efCPT);
         }
         if (bSeparate || bSplit)
@@ -1269,7 +1269,7 @@ int gmx_trjconv(int argc, char *argv[])
             useatoms.nr = nout;
         }
         /* select what to read */
-        if (ftp == efTRR || ftp == efTRJ)
+        if (ftp == efTRR)
         {
             flags = TRX_READ_X;
         }
@@ -1353,7 +1353,6 @@ int gmx_trjconv(int argc, char *argv[])
                     break;
                 case efXTC:
                 case efTRR:
-                case efTRJ:
                     out = NULL;
                     if (!bSplit && !bSubTraj)
                     {
@@ -1748,7 +1747,6 @@ int gmx_trjconv(int argc, char *argv[])
                                 write_tng_frame(trxout, &frout);
                                 // TODO when trjconv behaves better: work how to read and write lambda
                                 break;
-                            case efTRJ:
                             case efTRR:
                             case efXTC:
                                 if (bSplitHere)
diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index d5222db270..80a86c4df4 100644
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -2092,9 +2092,9 @@ int gmx_tune_pme(int argc, char *argv[])
         /* g_tune_pme */
         { efOUT, "-p",      "perf",     ffWRITE },
         { efLOG, "-err",    "bencherr", ffWRITE },
-        { efTPX, "-so",     "tuned",    ffWRITE },
+        { efTPR, "-so",     "tuned",    ffWRITE },
         /* mdrun: */
-        { efTPX, NULL,      NULL,       ffREAD },
+        { efTPR, NULL,      NULL,       ffREAD },
         { efTRN, "-o",      NULL,       ffWRITE },
         { efCOMPRESSED, "-x", NULL,     ffOPTWR },
         { efCPT, "-cpi",    NULL,       ffOPTRD },
diff --git a/src/gromacs/gmxana/gstat.h b/src/gromacs/gmxana/gstat.h
index bac6aeb270..0d490d9ab1 100644
--- a/src/gromacs/gmxana/gstat.h
+++ b/src/gromacs/gmxana/gstat.h
@@ -300,7 +300,6 @@ void read_ang_dih(const char *trj_fn,
  * Read a trajectory and calculate angles and dihedrals.
  *
  * trj_fn      file name of trajectory
- * tpb_fn      file name of tpb file
  * bAngles     do we have to read angles or dihedrals
  * bSaveAll    do we have to store all in the dih array
  * bRb         do we have Ryckaert-Bellemans dihedrals (trans = 0)
diff --git a/src/gromacs/gmxlib/main.cpp b/src/gromacs/gmxlib/main.cpp
index 799a41fa5a..dffa2ad7d8 100644
--- a/src/gromacs/gmxlib/main.cpp
+++ b/src/gromacs/gmxlib/main.cpp
@@ -101,7 +101,7 @@ static void par_fn(char *base, int ftp, const t_commrec *cr,
     strcat(buf, ".");
 
     /* Add extension again */
-    strcat(buf, (ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
+    strcat(buf, (ftp == efTPR) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
     if (debug)
     {
         fprintf(debug, "rank %d par_fn '%s'\n", cr->nodeid, buf);
@@ -396,7 +396,7 @@ void init_multisystem(t_commrec *cr, int nsim, char **multidirs,
              * at the actual file name
              */
             if (is_output(&fnm[i]) ||
-                fnm[i].ftp == efTPX || fnm[i].ftp == efCPT ||
+                fnm[i].ftp == efTPR || fnm[i].ftp == efCPT ||
                 strcmp(fnm[i].opt, "-rerun") == 0)
             {
                 ftp = fn2ftp(fnm[i].fns[0]);
diff --git a/src/gromacs/gmxpreprocess/grompp.c b/src/gromacs/gmxpreprocess/grompp.c
index d8cde70d4e..7e32feb2f6 100644
--- a/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@ -1534,7 +1534,7 @@ int gmx_grompp(int argc, char *argv[])
         { efNDX, NULL,  NULL,        ffOPTRD },
         { efTOP, NULL,  NULL,        ffREAD  },
         { efTOP, "-pp", "processed", ffOPTWR },
-        { efTPX, "-o",  NULL,        ffWRITE },
+        { efTPR, "-o",  NULL,        ffWRITE },
         { efTRN, "-t",  NULL,        ffOPTRD },
         { efEDR, "-e",  NULL,        ffOPTRD },
         /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
@@ -2083,7 +2083,7 @@ int gmx_grompp(int argc, char *argv[])
     }
 
     done_warning(wi, FARGS);
-    write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, &state, sys);
+    write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);
 
     /* Output IMD group, if bIMD is TRUE */
     write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.c
index ceb5ec2173..63fd7cffb1 100644
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.c
@@ -708,8 +708,8 @@ void chk_enx(const char *fn)
 int gmx_check(int argc, char *argv[])
 {
     const char     *desc[] = {
-        "[THISMODULE] reads a trajectory ([TT].trj[tt], [TT].trr[tt] or ",
-        "[TT].xtc[tt]), an energy file ([TT].ene[tt] or [TT].edr[tt])",
+        "[THISMODULE] reads a trajectory ([TT].tng[tt], [TT].trr[tt] or ",
+        "[TT].xtc[tt]), an energy file ([TT].edr[tt])",
         "or an index file ([TT].ndx[tt])",
         "and prints out useful information about them.[PAR]",
         "Option [TT]-c[tt] checks for presence of coordinates,",
@@ -725,8 +725,8 @@ int gmx_check(int argc, char *argv[])
         "file are indeed correct in the trajectory. If not you may have",
         "non-matching files due to e.g. deshuffling or due to problems with",
         "virtual sites. With these flags, [TT]gmx check[tt] provides a quick check for such problems.[PAR]",
-        "The program can compare two run input ([TT].tpr[tt], [TT].tpb[tt] or",
-        "[TT].tpa[tt]) files",
+        "The program can compare two run input ([TT].tpr[tt])",
+        "files",
         "when both [TT]-s1[tt] and [TT]-s2[tt] are supplied.",
         "Similarly a pair of trajectory files can be compared (using the [TT]-f2[tt]",
         "option), or a pair of energy files (using the [TT]-e2[tt] option).[PAR]",
@@ -738,8 +738,8 @@ int gmx_check(int argc, char *argv[])
     t_filenm        fnm[] = {
         { efTRX, "-f",  NULL, ffOPTRD },
         { efTRX, "-f2",  NULL, ffOPTRD },
-        { efTPX, "-s1", "top1", ffOPTRD },
-        { efTPX, "-s2", "top2", ffOPTRD },
+        { efTPR, "-s1", "top1", ffOPTRD },
+        { efTPR, "-s2", "top2", ffOPTRD },
         { efTPS, "-c",  NULL, ffOPTRD },
         { efEDR, "-e",  NULL, ffOPTRD },
         { efEDR, "-e2", "ener2", ffOPTRD },
@@ -796,7 +796,7 @@ int gmx_check(int argc, char *argv[])
     }
     else if (fn2)
     {
-        fprintf(stderr, "Please give me TWO trajectory (.xtc/.trr/.trj) files!\n");
+        fprintf(stderr, "Please give me TWO trajectory (.xtc/.trr/.tng) files!\n");
     }
 
     fn1 = opt2fn_null("-s1", NFILE, fnm);
@@ -819,7 +819,7 @@ int gmx_check(int argc, char *argv[])
     }
     else if ((fn1 && !opt2fn_null("-f", NFILE, fnm)) || (!fn1 && fn2))
     {
-        fprintf(stderr, "Please give me TWO run input (.tpr/.tpa/.tpb) files\n"
+        fprintf(stderr, "Please give me TWO run input (.tpr) files\n"
                 "or specify the -m flag to generate a methods.tex file\n");
     }
 
diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.c
index c70e194488..814f7ee1e4 100644
--- a/src/gromacs/tools/convert_tpr.c
+++ b/src/gromacs/tools/convert_tpr.c
@@ -374,11 +374,11 @@ int gmx_convert_tpr(int argc, char *argv[])
     char              buf[200], buf2[200];
     output_env_t      oenv;
     t_filenm          fnm[] = {
-        { efTPX, NULL,  NULL,    ffREAD  },
+        { efTPR, NULL,  NULL,    ffREAD  },
         { efTRN, "-f",  NULL,    ffOPTRD },
         { efEDR, "-e",  NULL,    ffOPTRD },
         { efNDX, NULL,  NULL,    ffOPTRD },
-        { efTPX, "-o",  "tpxout", ffWRITE }
+        { efTPR, "-o",  "tprout", ffWRITE }
     };
 #define NFILE asize(fnm)
 
@@ -423,7 +423,7 @@ int gmx_convert_tpr(int argc, char *argv[])
     bTime      = opt2parg_bSet("-time", asize(pa), pa);
     bTraj      = (opt2bSet("-f", NFILE, fnm) || bTime);
 
-    top_fn = ftp2fn(efTPX, NFILE, fnm);
+    top_fn = ftp2fn(efTPR, NFILE, fnm);
     fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);
 
     snew(ir, 1);
diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.c
index 86ba6ff95a..c87fe831ce 100644
--- a/src/gromacs/tools/dump.c
+++ b/src/gromacs/tools/dump.c
@@ -409,25 +409,20 @@ static void list_tng(const char gmx_unused *fn)
 
 void list_trx(const char *fn)
 {
-    int ftp;
-
-    ftp = fn2ftp(fn);
-    if (ftp == efXTC)
-    {
-        list_xtc(fn);
-    }
-    else if ((ftp == efTRR) || (ftp == efTRJ))
-    {
-        list_trn(fn);
-    }
-    else if (ftp == efTNG)
-    {
-        list_tng(fn);
-    }
-    else
+    switch (fn2ftp(fn))
     {
-        fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
-                fn, fn);
+        case efXTC:
+            list_xtc(fn);
+            break;
+        case efTRR:
+            list_trn(fn);
+            break;
+        case efTNG:
+            list_tng(fn);
+            break;
+        default:
+            fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
+                    fn, fn);
     }
 }
 
@@ -608,9 +603,9 @@ static void list_mtx(const char *fn)
 int gmx_dump(int argc, char *argv[])
 {
     const char *desc[] = {
-        "[THISMODULE] reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
-        "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]), an energy",
-        "file ([TT].ene[tt]/[TT].edr[tt]), or a checkpoint file ([TT].cpt[tt])",
+        "[THISMODULE] reads a run input file ([TT].tpr[tt]),",
+        "a trajectory ([TT].trr[tt]/[TT].xtc[tt]/[TT]/tng[tt]), an energy",
+        "file ([TT].edr[tt]) or a checkpoint file ([TT].cpt[tt])",
         "and prints that to standard output in a readable format.",
         "This program is essential for checking your run input file in case of",
         "problems.[PAR]",
@@ -622,7 +617,7 @@ int gmx_dump(int argc, char *argv[])
         "Position restraint output from -sys -s is broken"
     };
     t_filenm    fnm[] = {
-        { efTPX, "-s", NULL, ffOPTRD },
+        { efTPR, "-s", NULL, ffOPTRD },
         { efTRX, "-f", NULL, ffOPTRD },
         { efEDR, "-e", NULL, ffOPTRD },
         { efCPT, NULL, NULL, ffOPTRD },
@@ -648,9 +643,9 @@ int gmx_dump(int argc, char *argv[])
     }
 
 
-    if (ftp2bSet(efTPX, NFILE, fnm))
+    if (ftp2bSet(efTPR, NFILE, fnm))
     {
-        list_tpx(ftp2fn(efTPX, NFILE, fnm), bShowNumbers,
+        list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers,
                  ftp2fn_null(efMDP, NFILE, fnm), bSysTop);
     }
     else if (ftp2bSet(efTRX, NFILE, fnm))
diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index e2bc90d50d..901cccfdcd 100644
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -410,7 +410,7 @@ int gmx_mdrun(int argc, char *argv[])
     };
     t_commrec    *cr;
     t_filenm      fnm[] = {
-        { efTPX, NULL,      NULL,       ffREAD },
+        { efTPR, NULL,      NULL,       ffREAD },
         { efTRN, "-o",      NULL,       ffWRITE },
         { efCOMPRESSED, "-x", NULL,     ffOPTWR },
         { efCPT, "-cpi",    NULL,       ffOPTRD },
diff --git a/src/programs/mdrun/membed.c b/src/programs/mdrun/membed.c
index 758a5acc47..af701ac48f 100644
--- a/src/programs/mdrun/membed.c
+++ b/src/programs/mdrun/membed.c
@@ -1034,7 +1034,7 @@ gmx_membed_t init_membed(FILE *fplog, int nfile, const t_filenm fnm[], gmx_mtop_
         get_input(membed_input, &xy_fac, &xy_max, &z_fac, &z_max, &it_xy, &it_z, &probe_rad, &low_up_rm,
                   &maxwarn, &pieces, &bALLOW_ASYMMETRY);
 
-        tpr_version = get_tpr_version(ftp2fn(efTPX, nfile, fnm));
+        tpr_version = get_tpr_version(ftp2fn(efTPR, nfile, fnm));
         if (tpr_version < membed_version)
         {
             gmx_fatal(FARGS, "Version of *.tpr file to old (%d). "
diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index 0afd51b194..864b2b729e 100644
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -1103,7 +1103,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
     if (SIMMASTER(cr))
     {
         /* Read (nearly) all data required for the simulation */
-        read_tpx_state(ftp2fn(efTPX, nfile, fnm), inputrec, state, NULL, mtop);
+        read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, NULL, mtop);
 
         if (inputrec->cutoff_scheme != ecutsVERLET &&
             ((Flags & MD_TESTVERLET) || getenv("GMX_VERLET_SCHEME") != NULL))
diff --git a/src/programs/view/view.cpp b/src/programs/view/view.cpp
index 23a58df929..891cb1fd81 100644
--- a/src/programs/view/view.cpp
+++ b/src/programs/view/view.cpp
@@ -309,7 +309,7 @@ static void init_gmx(t_x11 *x11, char *program, int nfile, t_filenm fnm[],
     snew(gmx, 1);
     snew(gmx->wd, 1);
 
-    ePBC = read_tpx_top(ftp2fn(efTPX, nfile, fnm),
+    ePBC = read_tpx_top(ftp2fn(efTPR, nfile, fnm),
                         NULL, box, &natom, NULL, NULL, NULL, &top);
 
     read_first_frame(oenv, &status, ftp2fn(efTRX, nfile, fnm), &fr, TRX_DONT_SKIP);
@@ -365,7 +365,7 @@ static void init_gmx(t_x11 *x11, char *program, int nfile, t_filenm fnm[],
     init_dlgs(x11, gmx);
 
     /* Now do file operations */
-    set_file(x11, gmx->man, ftp2fn(efTRX, nfile, fnm), ftp2fn(efTPX, nfile, fnm));
+    set_file(x11, gmx->man, ftp2fn(efTRX, nfile, fnm), ftp2fn(efTPR, nfile, fnm));
 
     ShowDlg(gmx->dlgs[edFilter]);
 }
@@ -397,7 +397,7 @@ int gmx_view(int argc, char *argv[])
     output_env_t oenv;
     t_filenm     fnm[] = {
         { efTRX, "-f", NULL, ffREAD },
-        { efTPX, NULL, NULL, ffREAD },
+        { efTPR, NULL, NULL, ffREAD },
         { efNDX, NULL, NULL, ffOPTRD }
     };
 #define NFILE asize(fnm)