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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>So, what EXACTLY are you doing?<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>
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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>vivek sharma<br>
<b>Sent:</b> Monday, 25 January 2010 7:38 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Ligand coming out while trying Drug-enzyme
tutorial<o:p></o:p></span></p>
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<p class=MsoNormal>HI Tsjerk,<br>
Thanks for your reply. But, I can't see if it is going suddenly or gradually.<br>
What i can see is the ligand is away from the molecule after editing the gro
file with PRODRG output.<br>
<br>
It seems liek PRODRG has modified the co-ordinates that places ligand away from
the protein.<br>
<br>
~Vivek<o:p></o:p></p>
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<p class=MsoNormal>2010/1/25 Tsjerk Wassenaar <<a
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><o:p></o:p></p>
<p class=MsoNormal>Hi Vivek,<o:p></o:p></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><br>
> Now when I am processing the modified .gro file to generate box, the
ligand<br>
> and cofactor are going away from the protein molecule and I am not able to<br>
> analyze the complex.<o:p></o:p></p>
</div>
<p class=MsoNormal>Gradually going away, or suddenly jumping?<br>
<br>
In the latter case, read up on periodic boundary conditions.<br>
<span style='color:#888888'><br>
Tsjerk</span><o:p></o:p></p>
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<p class=MsoNormal><br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
--<o:p></o:p></p>
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<p class=MsoNormal>gmx-users mailing list <a
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