[gmx-users] (no subject)

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Mon Dec 2 21:13:04 CET 2002

Hi everybody,

I have the next error message when run grompp:

akilonia 35% grompp -f em.mdp -c ftsz_b4em.gro -p ftsz.top -o
                         :-)  G  R  O  M  A  C  S  (-:

                Gravel Rubs Often Many Awfully Cauterized Sores

                             :-)  VERSION 3.1  (-:

       Copyright (c) 1991-2002, University of Groningen, The Netherlands

         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.

    :-)  /usr/local/gromacs/3.1_sgi/mips-sgi-irix6.5/r10000/bin/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  ftsz_b4em.gro  Input         Generic structure: gro g96 pdb tpr
tpb tpa
  -r       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       ftsz.top  Input         Topology file
 -pp  processed.top  Output, Opt.  Topology file
  -o    ftsz_em.tpr  Output        Generic run input: tpr tpb tpa
  -t       traj.trr  Input, Opt.   Full precision trajectory: trr trj

      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
       -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]rmdumbds  bool    yes  Remove constant bonded interactions with
       -load string         Releative load capacity of each node on a
                            machine. Be sure to use quotes around the
                            which should contain a number for each node
    -maxwarn    int     10  Number of warnings after which input
-[no]check14   bool     no  Remove 1-4 interactions without Van der

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to #mdout.mdp#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
cpp: error /usr/local/gromacs/3.1_sgi/share/top/ff_dum.itp:1: DC_PO: too
much pushback

cpp exit code: 256
Tried to execute: '/lib/cpp -I../top
-I/usr/local/gromacs/3.1_sgi/share/top -DFLEX_SPC
 ftsz.top > grompp037882'
The '/lib/cpp' command is defined in the .mdp file
processing topology...
WARNING 1 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmx.itp", line
  Found another defaults entry, will use the last one
WARNING 2 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmx.itp", line
  Found another defaults entry, will use the last one
WARNING 3 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmxnb.itp", line
  Overriding atomtype O
WARNING 4 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmxnb.itp", line
  Overriding atomtype OM
WARNING 5 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmxnb.itp", line
  Overriding atomtype OA
WARNING 6 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmxnb.itp", line
  Overriding atomtype OW
WARNING 7 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmxnb.itp", line
  Overriding atomtype N
WARNING 8 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmxnb.itp", line
  Overriding atomtype NT
WARNING 9 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmxnb.itp", line
  Overriding atomtype NL
WARNING 10 [file "/usr/local/gromacs/3.1_sgi/share/top/ffgmxnb.itp",
line 14]:
  Overriding atomtype NR5
Cleaning up temporary file grompp037882
Fatal error: Too many warnings,
/grompp terminated

Do you think this is a problem of my molecule/topology, or a problem of
the gromacs installation??

Thanks a lot in advance,



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