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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>It is most likely due to having the order of your molecules in
the topology file (.top) different to those that are in coordinate file (.gro).<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:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Drug Delivery, Disposition and Dynamics</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><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'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
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>kecy_wu@sina.com<br>
<b>Sent:</b> Thursday, 22 April 2010 1:14 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] warning when process the files with grompp<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p> Hello, I want to generate the em.tpr file, but it arise the
warning like this :<o:p></o:p></p>
<p class=MsoNormal><em><span style='font-family:"SimSun","serif"'>Warning: atom
name 1 in TBP_wat.top and 10tbpc12wat1.gro does not match (C13 - OW)<o:p></o:p></span></em></p>
<p class=MsoNormal><em><span style='font-family:"SimSun","serif"'>Warning: atom
name 2 in TBP_wat.top and 10tbpc12wat1.gro does not match (C10 - HW1)<o:p></o:p></span></em></p>
<p class=MsoNormal><em><span style='font-family:"SimSun","serif"'>Warning: atom
name 3 in TBP_wat.top and 10tbpc12wat1.gro does not match (C7 - HW2)<o:p></o:p></span></em></p>
<p class=MsoNormal><em><span style='font-family:"SimSun","serif"'>Warning: atom
name 4 in TBP_wat.top and 10tbpc12wat1.gro does not match (C6 - OW)<o:p></o:p></span></em></p>
<p class=MsoNormal><em><span style='font-family:"SimSun","serif"'>Warning: atom
name 5 in TBP_wat.top and 10tbpc12wat1.gro does not match (O5 - HW1)<o:p></o:p></span></em></p>
<p class=MsoNormal><em><span style='font-family:"SimSun","serif"'>Warning: atom
name 6 in TBP_wat.top and 10tbpc12wat1.gro does not match (P1 - HW2)<o:p></o:p></span></em></p>
<p class=MsoNormal><em><span style='font-family:"SimSun","serif"'>Warning: atom
name 7 in TBP_wat.top and 10tbpc12wat1.gro does not match (O4 - OW)</span></em><o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>My system is water and dodecane (from 0 to 5 nm of the
z axis is water box, 5 to 10 nm dodecane box), and the TBP dissolves in the
dodecane, if I overlook it , mdrun can not do the energy minimization
well, and the TBP molecule will be tattered. <o:p></o:p></p>
<p> <o:p></o:p></p>
<p>I hope you can help me ,thank you very much!<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p> <o:p></o:p></p>
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