Hi Dallas,<br>I am trying to run MD simulation over a docked complex (protein+ligand), to confirm their dynamic stability in water media.<br>For the same I am using PRODRG server to generate topologies for ligand molecule as gromacs can generate topology for 20 standard residues. As mentioned in tutorial for drug-enzyme complex, I am editing the .top and .gro files to include the PRODRG generated files (DRGGMX.ITP in .top and DRGAPH.GRO in .gro file).<br>
I observe that their are changes in co-ordinate of ligand after processing them through PRODRG server. So these new co-ordinates for ligand are placing ligand away from the protein while the ligand molecule was in protein pocket in original docked complex.<br>
<br>I hope it gives what I am trying to do, and where I am getting stuck.<br><br>I am looking for some suggestions and more insight of the problem to solve it.<br>Earlier I have done same procedure successfully for a different docked complex.<br>
<br>Regards,<br>Vivek<br><br><div class="gmail_quote">2010/1/27 Dallas B. Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@pharm.monash.edu.au">Dallas.Warren@pharm.monash.edu.au</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div><div class="im">
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">So, what EXACTLY are you doing?</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span style="font-size: 10pt; color: rgb(31, 73, 125);">Drug Delivery, Disposition and Dynamics</span><span style="font-size: 10pt; color: rgb(31, 73, 125);"><br>
</span><span style="font-size: 10pt; color: rgb(31, 73, 125);">Monash Institute of Pharmaceutical Sciences</span><span style="font-size: 10pt; color: rgb(31, 73, 125);">,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@pharm.monash.edu.au" target="_blank">dallas.warren@pharm.monash.edu.au</a><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: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
</div><div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"><div class="im">
<div>
<div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;">
<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <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</span></p>
</div>
</div>
<p class="MsoNormal"> </p>
</div><p class="MsoNormal">HI Tsjerk,</p><div><div></div><div class="h5"><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</div></div><div><div></div><div class="h5">
<div>
<p class="MsoNormal">2010/1/25 Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></p>
<p class="MsoNormal">Hi Vivek,</p>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;"><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.</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: rgb(136, 136, 136);"><br>
Tsjerk</span></p>
<div>
<p class="MsoNormal"><br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
--</p>
</div>
<div>
<div>
<p class="MsoNormal">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></p>
</div>
</div>
</div>
<p class="MsoNormal"> </p>
</div></div></div>
</div>
</div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>