[gmx-users] Fatal error with grompp(with detail process)

Jenny Hsu jenny.h1087 at gmail.com
Fri Nov 28 08:58:41 CET 2008

Hi all:
I have a problem with grompp
I want to making "POPC+protein" file
and I search the archieve and follow the process
1.run pdb2gmx for protein only
2.add below parameters into my topology file
 #include "ffG53a6.itp"
 #include "lipid.itp"
 #include "popc.itp"
3.adjust the [ molecules ] section to list the number and type of my
4.run editconf and genbox
5.run grompp and it shows
Fatal error:
Atomtype CA not found

*Below is all information it shows*
*Can someone help me to solve this problem?*
*I am appreciate with that.*
        :-)  G  R  O  M  A  C  S  (-:
        Getting the Right Output Means no Artefacts in Calculating Stuff
                             :-)  VERSION 4.0  (-:
      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, 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 1UEO-nowater_water.gro  Input        Structure file: gro g96 pdb tpr
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
-rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt.  Index file
  -p 1UEO-nowater.top  Input        Topology file
-pp  processed.top  Output, Opt. Topology file
  -o 1UEO-nowater_em.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file: edr ene
Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-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.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
-maxwarn     int    0       Number of allowed warnings during input
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error
-[no]renum   bool   yes     Renumber atomtypes and minimize number of
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/md/share/gromacs/top/ffG53a6.itp
Opening library file /usr/local/md/share/gromacs/top/ffG53a6nb.itp
Opening library file /usr/local/md/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/local/md/share/gromacs/top/ff_dum.itp
WARNING 1 [file lipid.itp, line 14]:
  Overriding atomtype LO
WARNING 2 [file lipid.itp, line 15]:
  Overriding atomtype LOM
WARNING 3 [file lipid.itp, line 16]:
  Overriding atomtype LNL
WARNING 4 [file lipid.itp, line 17]:
  Overriding atomtype LC
WARNING 5 [file lipid.itp, line 18]:
  Overriding atomtype LH1
WARNING 6 [file lipid.itp, line 19]:
  Overriding atomtype LH2
WARNING 7 [file lipid.itp, line 20]:
  Overriding atomtype LP
WARNING 8 [file lipid.itp, line 21]:
  Overriding atomtype LOS
WARNING 9 [file lipid.itp, line 22]:
  Overriding atomtype LP2
WARNING 10 [file lipid.itp, line 23]:
  Overriding atomtype LP3
WARNING 11 [file lipid.itp, line 24]:
  Overriding atomtype LC3
WARNING 12 [file lipid.itp, line 25]:
  Overriding atomtype LC2
WARNING 13 [file lipid.itp, line 108]:
  Overriding non-bonded parameters,
  old: 0.00238804 3.38411e-06 new
LNL     C   1   2.387718e-03 2.389594e-06
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 793
Fatal error:
Atomtype CA not found

Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
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