[gmx-users] Error running grompp

fufengliu at tju.edu.cn fufengliu at tju.edu.cn
Fri Jul 6 08:03:57 CEST 2007

Dear gmx users:
        I m carrying a protein explicit solvent simulation  using gromacs  3.3,
then i added water, but in next step, I m getting the following error,

 grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr
                         :-)  G  R  O  M  A  C  S  (-:

        Getting the Right Output Means no Artefacts in Calculating Stuff

                            :-)  VERSION 3.3.1  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, The GROMACS development team,
            check out http://www.gromacs.org for
 more information.

         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         em.mdp  Input, Opt!  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c        try.gro  Input        Generic structure: gro g96 pdb tpr tpb tpa
  -r       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
 -rb       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          A.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o       A_em.tpr  Output       Generic run input: tpr tpb tpa xml
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj
  -e       ener.edr  Input, Opt.  Generic energy: edr ene

      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]rmvsbds   bool    yes  Remove constant bonded interactions with virtual
       -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
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals
  -[no]renum   bool    yes  Renumber atomtypes and minimize number of

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
Cleaning up temporary file grompp3wF5if
Program grompp, VERSION 3.3.1
Source code file: toputil.c, line: 61

Fatal error:
Atomtype 'C3' not found!

"Baby, It Aint Over Till It's Over" (Lenny Kravitz)
Can you tell me how to correct it?
Best Regards!
Fufeng liu

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