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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Only run pdb2gmx on a single molecule of interest, which then generates
a topology file that you can use (with slight modification) for a simulation
with a single molecule, or many. Keep the topology to the side and don’t
run pdb2gmx again. There is no need to, you already have the topology
information for the entire molecule. If you then add more than one to the
coordinate box, GROMACS will know from that topology how things interact, since
it is exactly the same molecule, just many copies of it.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><br>
Then you take the coordinate file, make multiple copies of the molecule as
required, then adjust your topology file to show the correct number of
molecules. Originally it will say 1 molecule. If you say make a coordinate
file with a total of 8 molecules, then you will need to change that number in
the [ molecules ] section from 1 to 8 i.e.<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'>Original .top<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> [ molecules ]<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Protein 1<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'>Multiple molecule .top<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>[ molecules ]<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Protein 8<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>
<div>
<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>
</div>
<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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<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<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 11:22 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>
<pre>"""<br>
Were all of your termini treated correctly here? If you pass multiple chains to <o:p></o:p></pre><pre>pdb2gmx, the potential problem is that pdb2gmx will read the entire structure as <o:p></o:p></pre><pre>one protein, thus trying to connect sequential N- and C-termini. This is why <o:p></o:p></pre><pre>the example on the wiki is pertinent - generate a topology for a single <o:p></o:p></pre><pre>polypeptide, then (in your case) change the [molecules] section to reflect the <o:p></o:p></pre><pre>fact that you're building a system with 8 protein molecules (instead of just 1). <o:p></o:p></pre><pre> Use the pdb2gmx-processed coordinate file as input into genconf and so forth.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>-Justin<br>
"""<o:p></o:p></pre>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'><br>
<br>
I'm lost :(<br>
<br>
I have a feeling that pdb2gmx is probably converting it to one big protein.<br>
<br>
Procedure at this point.<br>
<br>
genconf -f polygly.pdb -nbox 2 2 2 -shuffle -o did_it_work.pdb<br>
<br>
pdb2gmx -f polygly.pdb -p polygly.top -o polygly.gro<br>
<br>
0: GROMOS96 43a1 force field<br>
<br>
vi polygly.top<br>
Changed proteins to 8<br>
<br>
At this point I have no clue what to do....<o:p></o:p></span></p>
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