[gmx-users] Atomtype not found

Patrick Ladam ladam at smbh.smbh.univ-paris13.fr
Mon Jul 8 22:14:54 CEST 2002

Hi all,
I am on my way of trying to simply minimize a DNA model with all hydrogen atoms
At that point I am building my own version of ffgmx2 with missing hydrogen

1) I succeeded in building a topology file using pdb2gmx. This topology file
bonding of all hydrogens to their heavy atoms. For instance I have H5*1 and H5*2

bonded to C5* (that is H5' and H5" to C5') in the top file.

2) Happy with that, I try to run an energy minimisation using this top file and
here is the error
message I get concerning atomtype C5* not found (see last line):

tintin pl 75>grompp -f em.mdp -p my.top -c psn1_2.gro -o psn1_em2.tpr
                         :-)  G  R  O  M  A  C  S  (-:

        Getting the Right Output Means no Artefacts in Calculating Stuff

                             :-)  VERSION 3.1  (-:

       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  (-:

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     psn1_2.gro  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         my.top  Input         Topology file
 -pp  processed.top  Output, Opt.  Topology file
  -o   psn1_em2.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
-[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: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file grompp002001
Fatal error: Atomtype 'C5*' not found!
tintin pl 76>

I have been looking in the itp file (where atomtypes are defined)

and HC (atomtype for H5*1 and H5*2) and CS2 (atomtype for C5*) are


So at that point I don't have a clue why grompp stops...Can anyone

help me on that, the error message is not very informative to me, so...

Bye and thanX

| Patrick LADAM                   |                               |
| Laboratoire CSSB                |     THE BIG BANG THEORY:      |
| UFR SMBH                        |                               |
| 74 rue Marcel Cachin            |   In the begining there was   |
| 93017 Bobigny CEDEX             |        nothing at all.        |
| >>> NEW e-mail: <<<             |                               |
| ladam at smbh.smbh.univ-paris13.fr |      Then, it exploded...     |
| Tel: 01 48 38 77 26 / 76 85     |                               |
| Fax: 01 48 38 77 77             |                               |

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