Dear all gromacs users,<br> <br> I tried the "grompp -c 3I40_ion.gro -p 3I40.top -o 3I40_b4em.tpr -f em.mdp" and i got the following error. <br><div id=":14i"> <br>
<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f em.mdp Input grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br>
-c 3I40_ion.gro Input Structure file: gro g96 pdb tpr etc.<br> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.<br> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.<br>
-n index.ndx Input, Opt. Index file<br> -p 3I40.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br> -o 3I40_b4em.tpr Output Run input file: tpr tpb tpa<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>
-e ener.edr Input, Opt. Energy file<br><br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-[no]version bool no Print version info and quit<br>
-nice int 0 Set the nicelevel<br>-[no]v bool no Be loud and noisy<br>-time real -1 Take frame at or first after this time.<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br>
sites<br>-maxwarn int 0 Number of allowed warnings during input<br> processing. Not for normal use and may generate<br> unstable systems<br>
-[no]zero bool no Set parameters for bonded interactions without<br> defaults to zero instead of generating an error<br>-[no]renum bool yes Renumber atomtypes and minimize number of<br>
atomtypes<br><br>Ignoring obsolete mdp entry 'cpp'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.19#<br>Generated 279 of the 1225 non-bonded parameter combinations<br><br>
-------------------------------------------------------<br>Program grompp, VERSION 4.5.5<br>Source code file: toppush.c, line: 1228<br><br><br><br>Fatal error:<br>moleculetype CU1 is redefined.<br><br>Is there any explanation why is thid happening?<br>
<br>I would appreciate any help. Iam new in using MD and gromac in particular.<br><br>Suryanarayana Seera,<br>PhD student,<br>Hyderabad,<br>India.<br></div>