[gmx-users] Regarding error

Seera Suryanarayana palusoori at gmail.com
Tue May 29 09:02:08 CEST 2012

Dear all gromacs users,

                        I tried the  "grompp -c 3I40_ion.gro -p 3I40.top -o
3I40_b4em.tpr -f em.mdp" and i got the following error.

Option     Filename  Type         Description
  -f         em.mdp  Input        grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c   3I40_ion.gro  Input        Structure file: gro g96 pdb tpr etc.
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n      index.ndx  Input, Opt.  Index file
  -p       3I40.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o  3I40_b4em.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-[no]v       bool   no      Be loud and noisy
-time        real   -1      Take frame at or first after this time.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
-maxwarn     int    0       Number of allowed warnings during input
                            processing. Not for normal use and may generate
                            unstable systems
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error
-[no]renum   bool   yes     Renumber atomtypes and minimize number of

Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.19#
Generated 279 of the 1225 non-bonded parameter combinations

Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1228

Fatal error:
moleculetype CU1 is redefined.

Is there any explanation why is thid happening?

I would appreciate any help. Iam new in using MD and gromac in particular.

Suryanarayana Seera,
PhD student,
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