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.
Cheers, Emmanuel ========================================================= 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.bi...@monash.edu<mailto:firstname.lastn...@monash.edu> www.pharm.monash.edu.au<http://www.pharm.monash.edu.au/> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Seera Suryanarayana Sent: Tuesday, 29 May 2012 5:02 PM To: gmx-users@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 sites -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 atomtypes 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, Hyderabad, India.
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