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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Emmanuel<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial Narrow","sans-serif";color:black">=========================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Emmanuel Birru<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">PhD Candidate<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Faculty of Pharmacy and Pharmaceutical Sciences<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Monash University (Parkville Campus)<br>
381 Royal Parade, Parkville<br>
Victoria 3052, Australia<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">Tel: Int + 61 3 9903 9187<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black">E-mail:
</span><span lang="EN-US" style="font-family:"Calibri","sans-serif";color:#1F497D"><a href="mailto:firstname.lastname@monash.edu"><span lang="EN-AU" style="color:blue">emanuel.birru@monash.edu</span></a></span><span lang="EN-US" style="font-family:"Calibri","sans-serif";color:black">
</span><span style="font-family:"Calibri","sans-serif";color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:black"><a href="http://www.pharm.monash.edu.au/"><span style="color:blue">www.pharm.monash.edu.au</span></a><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Seera Suryanarayana<br>
<b>Sent:</b> Tuesday, 29 May 2012 5:02 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Regarding error<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.
<o:p></o:p></p>
<div id=":14i">
<p class="MsoNormal"> <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.<o:p></o:p></p>
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