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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