Option     Filename  Type          Description
------------------------------------------------------------
  -f         em.mdp  Input, Opt!   grompp input file with MD parameters
 -po      mdout.mdp  Output        grompp input file with MD parameters
  -c MeCO_Met_NHMe.pdb  Input         Generic structure: gro g96 pdb tpr tpb
                                   tpa
  -r       conf.gro  Input, Opt.   Generic structure: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt.   Index file
-deshuf  deshuf.ndx  Output, Opt.  Index file
  -p MeCO_Met_NHMe.top  Input         Topology file
 -pp  processed.top  Output, Opt.  Topology file
  -o MeCO_Met_NHMe.tpr  Output        Generic run input: tpr tpb tpa
  -t       traj.trr  Input, Opt.   Full precision trajectory: trr trj

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int      0  Set the nicelevel
      -[no]v   bool    yes  Be loud and noisy
       -time   real     -1  Take frame at or first after this time.
         -np    int      1  Generate statusfile for # nodes
-[no]shuffle   bool     no  Shuffle molecules over nodes
   -[no]sort   bool     no  Sort molecules according to X coordinate
-[no]rmdumbds  bool    yes  Remove constant bonded interactions with dummies
       -load string         Releative load capacity of each node on a parallel
                            machine. Be sure to use quotes around the string,
                            which should contain a number for each node
    -maxwarn    int     10  Number of warnings after which input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals


Back Off! I just backed up mdout.mdp to #mdout.mdp#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
WARNING 1 [file "MeCO_Met_NHMe.top", line 102]:
  No default Improper Dih. types, using zeroes
WARNING 2 [file "MeCO_Met_NHMe.top", line 103]:
  No default Improper Dih. types, using zeroes
WARNING 3 [file "MeCO_Met_NHMe.top", line 105]:
  No default Improper Dih. types, using zeroes
processing coordinates...
Fatal error: number of coordinates in coordinate file (MeCO_Met_NHMe.pdb, 16)
             does not match topology (MeCO_Met_NHMe.top, 0)
                         :-)  G  R  O  M  A  C  S  (-:

           Glycine aRginine prOline Methionine Alanine Cystine Serine

                            :-)  VERSION 3.1.1  (-:


       Copyright (c) 1991-2002, University of Groningen, The Netherlands
         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                                :-)  grompp  (-:

creating statusfile for 1 node...
calling /usr/libexec/gcc/darwin/ppc/2.95.2/cpp...
processing topology...