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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Note that the genbox box stacking you are using here is not
necessarily what you want. What sort of starting configuration do you want?
Is the concentration / spacing that you get when you stack boxes like that,
actually what you want? Or do you want a more concentrated type of system
where the molecules are intertwined etc.?<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>
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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 11:57 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>"""<o:p></o:p></pre><pre>genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Have you done any basic tutorial material before diving head-first into this <o:p></o:p></pre><pre>more complicated topic?<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>The idea is this: pdb2gmx generates the topology for the protein. You can then <o:p></o:p></pre><pre>do whatever you choose with this definition of a protein. After pdb2gmx, you <o:p></o:p></pre><pre>also have a coordinate file that meets force field specifications as far as <o:p></o:p></pre><pre>protonation goes. This is the set of coordinates you should replicate, since it <o:p></o:p></pre><pre
style='margin-bottom:12.0pt'>is correct within the force field.<br>
"""<br>
<br>
I've done all the tutorial material hat is supplied with Gromacs...<br>
<br>
I believe I may have got it. These are the steps I took.<br>
<br>
pdb2gmx -f polygly.pdb -p polygly.top -o polygly.gro<br>
<br>
vi polygly.top<br>
Changed Protein count from 1 to 8<br>
<br>
genconf -f polygly.gro -nbox 2 2 2 -o polygly_8.gro<br>
<br>
editconf -f polygly_8 -o -d 1.0<br>
<br>
genbox -cp out -cs -p polygly -o b4em<br>
<br>
grompp -v -f em -c b4em -o em -p polygly<br>
<br>
mdrun -v -s em -o em -c after_em -g emlog<br>
<br>
grompp -f pr -o pr -c after_em -r after_em -p polygly<br>
<br>
mdrun -v -s pr -e pr -o pr -c after_pr -g prlog >& pr.job &<br>
<br>
grompp -v -f full -o full -c after_pr -p polygly<br>
<br>
mdrun -v -s full -e full -o full -c after_full -g flog >& full.job &<br>
<br>
When I look at the simulation:<br>
<br>
ngmx -s pr -full<br>
<br>
There are 8 short peptides.<br>
<br>
Does anything seem wrong with these steps?<br>
<br>
Justin, thanks for the help :)<o:p></o:p></pre></div>
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