[gmx-users] grompp not running - please advise

[Jaimin Shah]

Dear all,
I just finished gromacs-3.2.1 installation and want to do teh examples.
The simulation of water did not run due to some unknown reason. Please see
below:
----------------------------------------------------------------------------

[root at localhost water]# grompp -f grompp.mdp -p topol.top -c spc216.pdb -o
water.tpr
                         :-)  G  R  O  M  A  C  S  (-:

               Go Rough, Oppose Many Angry Chinese Serial killers

                            :-)  VERSION 3.0.5  (-:

       Copyright (c) 1991-2001, 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  (-:

Option     Filename  Type          Description
------------------------------------------------------------
  -f     grompp.mdp  Input         grompp input file with MD parameters
 -po      mdout.mdp  Output        grompp input file with MD parameters
  -c     spc216.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      topol.top  Input         Topology file
 -pp  processed.top  Output, Opt.  Topology file
  -o      water.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

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to #mdout.mdp#
Warning 1 [file grompp.mdp, line unknown]:
  Unknown left-hand init_step in parameter file

Warning 2 [file grompp.mdp, line unknown]:
  Unknown left-hand comm-mode in parameter file

Warning 3 [file grompp.mdp, line unknown]:
  Unknown left-hand fcstep in parameter file

Warning 4 [file grompp.mdp, line unknown]:
  Unknown left-hand nbfgscorr in parameter file

Warning 5 [file grompp.mdp, line unknown]:
  Unknown left-hand nstcheckpoint in parameter file

Warning 6 [file grompp.mdp, line unknown]:
  Unknown left-hand table-extension in parameter file

Warning 7 [file grompp.mdp, line unknown]:
  Unknown left-hand ewald_geometry in parameter file

Warning 8 [file grompp.mdp, line unknown]:
  Unknown left-hand gb_algorithm in parameter file

Warning 9 [file grompp.mdp, line unknown]:
  Unknown left-hand nstgbradii in parameter file

Warning 10 [file grompp.mdp, line unknown]:
  Unknown left-hand rgbradii in parameter file

Fatal error: Too many warnings, grompp terminated
----------------------------------------------------------------------------
Can someone tell what is happening and how to remedy it?

Sincerely,
Jaimin Shah
Junior Research Fellow
Dr. Dulal Panda's Laboratory
School of Biosciences & Bioengineering
I.I.T. Bombay