[gmx-users] Fatal error: moleculetype CU1+ is redefined

[Sridhar Acharya]

Hi GMXusers,

I am facing a problem with the latest version of the GROMACS. When I 
generate the tpr file with grompp, I get the following error.
"Fatal error: moleculetype CU1+ is redefined"
The error is repeating with any molecule simulation that I try. Why is 
this error caused.
Waiting for your suggessions.
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               :-)  /home2/sridhar/bin/GROMACS3.3/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   1AZV_ion.gro  Input        Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -r       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
 -rb       conf.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -n      index.ndx  Input, Opt.  Index file
-deshuf  deshuf.ndx  Output, Opt. Index file
  -p       1AZV.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o  1AZV_b4em.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
                            sites
       -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
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals
  -[no]renum   bool    yes  Renumber atomtypes and minimize number of
                            atomtypes

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
WARNING 1 [file ../em.mdp, line unknown]:
  Unknown left-hand 'define' in parameter file

checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Cleaning up temporary file gromppVG7rEt
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 887

Fatal error:
moleculetype CU1+ is redefined
-------------------------------------------------------

"A Lady Shaves Her Legs" (C. Meijering)
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