[gmx-users] Regarding error

Emanuel Birru Emanuel.Birru at monash.edu
Tue May 29 09:28:52 CEST 2012

I guess you have duplicate the "moleculetype" entries for CU1 in your topology file. Check your topology file again. You can not  have more than one "moleculetype" definition per molecule type.


Emmanuel Birru
PhD Candidate

Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

Tel: Int + 61 3 9903 9187
E-mail: emanuel.birru at monash.edu<mailto:firstname.lastname at monash.edu>

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Seera Suryanarayana
Sent: Tuesday, 29 May 2012 5:02 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Regarding error

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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