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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Was your single molecule coordinate file energy minimised?<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'>Did you look at the coordinate file for multiple molecules?<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'>In your grompp step before em, what is that coordinate file you
are feeding to it? It has a different name to the one you generated using
genconf.<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><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class=MsoNormal><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@monash.edu<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>+61 3 9909 9304<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>
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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>
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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>C Johnson<br>
<b>Sent:</b> Thursday, 16 September 2010 10:06 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Re Multiple Chains<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'>Sorry guys, I'm still learning the lingo.<br>
<br>
I want to simulate multiple molecules.<br>
<br>
This is what I tried:<br>
<br>
genconf -f polygly.pdb -nbox 2 2 2 -shuffle -o did_it_work.pdb<br>
<br>
Does this even seem like the right thing to do?<br>
<br>
I got to this part:<br>
<span style='color:black'><br>
grompp -v -f em -c b4em -o em -p speptide <br>
mdrun -v -s em -o em -c after_em -g emlog </span><br>
<br>
But I get an error that essentially tells me that my system needs to be energy
minimized:<br>
<br>
Range checking error:<br>
Explanation: During neighborsearching, we assign each particle to a grid<br>
based on its coordinates. If your system contains collisions or parameter<br>
errors that give particles very high velocities you might end up with some<br>
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>
put these on a grid, so this is usually where we detect those errors.<br>
Make sure your system is properly energy-minimized and that the potential<br>
energy seems reasonable before trying again.<br>
<br>
Variable ci has value -2147483648. It should have been within [ 0 .. 150 ]<br>
<br>
<br>
I'm guessing I'm pretty wrong in my approach to adding multiple molecules based
on a single molecule pdb file. I'm determined to get this :)<br>
<br>
<o:p></o:p></span></p>
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