[gmx-users] error in ffgmxbon.itp

delara aghaie d_aghaie at yahoo.com
Sat Jan 8 10:44:46 CET 2011

Dear Justin
I want to run a simulation on a system containing DPPC and water(TIP4P-2005).
I have in my .top file some included .itp files.
they are:
ffgmx-local.itp (this is the name which we have selected for the modified version of ffgmx.itp)
in which they are two included files: ffgmxbon-local.itp & ffgmxnb-local.itp
I have simulated this system at 310 K without error before. Now I only changed the temp to 270 K in the run.mdp file, now using the grompp command I get this error:(I sent you the command line and the error, below) I do not now what is ffdum.itp (you can see error line below)
you can see below also the part of ffgmx-local.itp which the error is about that part.
please let me know how to fix the error.
thanks for your time

-bash-3.2$ grompp_mpi -c confout-310-500.gro -f run.mdp -n index.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 confout-310-500.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      index.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.2#
checking input for internal consistency...
calling cpp...
In file included from ffgmx-local.itp:9,
                 from topoldppc.top:3:
ffgmxbon-local.itp:125:22: error: ff_dum.itp: No such file or directory
cpp exit code: 256
Tried to execute: 'cpp  -I/apps/gromacs/3.3/share/top  topoldppc.top > gromppAjujan'
The 'cpp' command is defined in the .mdp file
processing topology...
ERROR 1 [file "ffgmxbon-local.itp", line 129]:
  Not enough parameters
ERROR 2 [file "ffgmxbon-local.itp", line 130]:
  Not enough parameters
ERROR 3 [file "ffgmxbon-local.itp", line 131]:
  Not enough parameters
ERROR 4 [file "ffgmxbon-local.itp", line 132]:
  Not enough parameters
ERROR 5 [file "ffgmxbon-local.itp", line 133]:
  Not enough parameters
ERROR 6 [file "ffgmxbon-local.itp", line 134]:
  Not enough parameters
ERROR 7 [file "ffgmxbon-local.itp", line 136]:
  Not enough parameters
ERROR 8 [file "ffgmxbon-local.itp", line 137]:
  Not enough parameters
ERROR 9 [file "ffgmxbon-local.itp", line 138]:
  Not enough parameters
ERROR 10 [file "ffgmxbon-local.itp", line 139]:
  Not enough parameters
Cleaning up temporary file gromppAjujan
Program grompp_mpi, VERSION 3.3
Source code file: fatal.c, line: 416
Fatal error:
Too many warnings, grompp_mpi terminated
Thanx for Using GROMACS - Have a Nice Day

[ constrainttypes ]
; now the constraints for the rigid NH3 groups
 MNH3    C    2   DC_MNC1                    line :129
 MNH3   CB    2   DC_MNC1
 MNH3  CHE    2   DC_MNC1
 MNH3  CH1    2   DC_MNC2
 MNH3  CH2    2   DC_MNC2
 MNH3 MNH3    2   DC_MNMN
; and the angle-constraints for OH and SH groups in proteins:
  CH2   HS    2   DC_CS                      line 136
  CH2   HO    2   DC_CO
  CH1   HO    2   DC_CO
   CB   HO    2   DC_CO
   C    HO    2   DC_CO
   P    HO    2   DC_PO



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