[gmx-users] error when running grompp

delara aghaie d_aghaie at yahoo.com
Tue Apr 26 22:21:01 CEST 2011

Dear Gromacs users
I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg and 16 Cl ions using genion and now want to use grompp and then start the simulation to see the effect of ions on the pressure-area isotherm of the system.
running grompp in gromacs 3.3 I see he following error:
please help em to solve it.let me knoe please what is cpp?
Thanks in advance
D. Aghaie
-bash-3.2$ grompp_mpi -c dppc-salt-Mg-0.1.gro -f run.mdp -n indexsalt-Mg.ndx -p topoldppc.top -o topol.tpr -np 8
                         :-)  G  R  O  M  A  C  S  (-:
                   Groningen Machine for Chemical Simulation
                             :-)  VERSION 3.3  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, 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_mpi  (-:
Option     Filename  Type         Description
  -f        run.mdp  Input, Opt!  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c dppc-salt-Mg-0.1.gro  Input        Generic structure: gro g96 pdb tpr
                                   tpb tpa xml
  -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 indexsalt-Mg.ndx  Input, Opt!  Index file
-deshuf  deshuf.ndx  Output, Opt. Index file
  -p  topoldppc.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o      topol.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      8  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 8 nodes...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling cpp...
topoldppc.top:7:20: error: ions.itp: No such file or directory
cpp exit code: 256
Tried to execute: 'cpp  -I/apps/gromacs/3.3/share/top  topoldppc.top > gromppzVWhWp'
The 'cpp' command is defined in the .mdp file
processing topology...
Generated 1369 of the 2211 non-bonded parameter combinations
Excluding 3 bonded neighbours for DPP 64
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 4152
turning all bonds into constraints...
Cleaning up temporary file gromppzVWhWp
Program grompp_mpi, VERSION 3.3
Source code file: toppush.c, line: 1264
Fatal error:
No such moleculetype Mg
Thanx for Using GROMACS - Have a Nice Day
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