[gmx-users] no coordinates in .top file

Owen, Michael MichaelOwen at creighton.edu
Tue Oct 10 20:36:57 CEST 2006

Hello gmx users,

here is the command that I used to run the preprocessor for my TFE molecule:   

           grompp -f em -v -o em -c tfe -p tfe_mike.top                        

and the output is pasted below.

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

               Go Rough, Oppose Many Angry Chinese Serial killers

                            :-)  VERSION 3.3.1  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, 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        tfe.gro  Input        Generic structure: gro g96 pdb tpr tpb tpa
  -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   tfe_mike.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o         em.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...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /lib/cpp...
tfe_mike.top:67:1: unterminated #ifdef
cpp exit code: 256
Tried to execute: '/lib/cpp  -I/usr/local/gromacs/share/gromacs/top -DPOSRE tfe_mike.top > grompppUuhtO'
The '/lib/cpp' command is defined in the .mdp file
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
processing coordinates...
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (tfe.gro, 9)
             does not match topology (tfe_mike.top, 0)

"I'm Only Faking When I Get It Right" (Soundgarden)

Thank you very muc for your help.


Michael Owen

Message: 1
Date: Tue, 10 Oct 2006 16:59:26 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] RE: no coordinates in .top file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <452BB54E.80206 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Owen, Michael wrote:
> Fellow gmx users,
> thanks for the suggestion, however, applying -v to grompp did not yield
> any additional information.  Shouldn't grompp read the number of
> coordinates from the list of atoms in the [ atoms ] section?  Could
> something be wrong with my .itp file?  Could it be that my .top and .itp
> files are in my working directory instead of the Gromacs "share" directory?

no, the problem is most likely in your topology.
post the output from grompp -v if you can not find the answer yourself.

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