[gmx-users] Error in .top file for grompp

한상화 hansh at kangwon.ac.kr
Thu Jan 4 06:25:08 CET 2007

Dear Gromacs users,


I have gone through all the way to the final product MD, where I received
the following error message for grompp.

The same topology file pn.top did not give me any problem in the previous
steps including grompp with pr.mdp or grompp with em.mdp.

I included solvent and ions in the md.mdp file for temperature control.

Any comments would be greatly appreciated.


Sanghwa Han

Dept of Biochemistry

Kangwon National University

Chunchon 200-701, South Korea



[root at cc papain]# grompp -f md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top -o



                         :-)  G  R  O  M  A  C  S  (-:


                  Gromacs Runs On Most of All Computer Systems


                             :-)  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  (-:


Option     Filename  Type         Description


  -f      pn_md.mdp  Input, Opt!  grompp input file with MD parameters

 -po      mdout.mdp  Output       grompp input file with MD parameters

  -c      pn_md.pdb  Input        Generic structure: gro g96 pdb tpr tpb tpa


  -r      pn_md.pdb  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         pn.top  Input        Topology file

 -pp  processed.top  Output, Opt. Topology file

  -o      pn_md.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

       -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...

' for variable integrator, using 'md'

Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'

' for variable ns-type, using 'Grid'

Next time use one of: 'Grid' 'Simple'

' for variable coulombtype, using 'Cut-off'

Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-
Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-
Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User'

' for variable optimize_fft, using 'no'

Next time use one of: 'no' 'yes'

' for variable tcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'

' for variable Pcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'

' for variable gen-vel, using 'no'

Next time use one of: 'no' 'yes'

' for variable constraints, using 'none'

Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

WARNING 1 [file pn_md.mdp, line unknown]:

  Unknown left-hand 'warnings' in parameter file


checking input for internal consistency...

....ling /usr/bin/cpp

: no such file or directory

cpp: warning: `-x c' after last input file has no effect

cpp: no input files

cpp exit code: 256

  -I/usr/share/gromacs/top  pn.top > gromppDJ5J3m'

' command is defined in the .mdp file

processing topology...

processing coordinates...


Program grompp, VERSION 3.3

Source code file: grompp.c, line: 427


Fatal error:

number of coordinates in coordinate file (pn_md.pdb, 34158)

             does not match topology (pn.top, 0)



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