Hi all<div><br></div><div>I was wondering if some body has done simulating multiple copies of small lead like fragments in a solvated box .</div><div><br></div><div>I want to soak my proteins with multiple copies of diverse fragments along with water as iam interested in finding the hot spots in proteins that can be successfully employed for fragment based drug design. The approach is analogs to the MCSS approach developed by Prof Karplus and the recent SILCS approach by Prof Mackerell.</div>
<div><br></div><div>The impediments which i theoretically fore see are</div><div>1) how to negate interactions terms between two fragments as two fragments may be competing for the same site.</div><div>2) How to create multiple topologies for multiple copies of the same fragment randomly placed all over the fragment</div>
<div>3) Iam also skeptical whether the fragments will be able to find their respective binding site in a nanosecond time scale when started De Novo contrary to the well settled proposition of docking and keeping the fragment in the active site. A look at this paper by DE Shaw " <span style="background-color:rgb(255,255,255);font-family:'Trebuchet MS',Arial,Helvetica,sans-serif;font-size:1.15em;line-height:1.4em;text-align:left">How Does a Drug Molecule Find Its Target Binding Site??" reveals the binding event to be captured on a mili second time second.</span></div>
<div><span style="background-color:rgb(255,255,255);font-family:'Trebuchet MS',Arial,Helvetica,sans-serif;font-size:1.15em;line-height:1.4em;text-align:left"><br></span></div><div><span style="background-color:rgb(255,255,255);text-align:left"><font face="'Trebuchet MS', Arial, Helvetica, sans-serif"><span style="font-size:1.15em;line-height:1.4em">Thanking you in advance for all thought provoking suggestions</span><span style="font-size:15px;line-height:20px">.</span></font></span></div>
<div><span style="background-color:rgb(255,255,255);text-align:left"><font face="'Trebuchet MS', Arial, Helvetica, sans-serif"><span style="font-size:15px;line-height:20px"><br></span></font></span></div><div><span style="background-color:rgb(255,255,255);text-align:left"><font face="'Trebuchet MS', Arial, Helvetica, sans-serif"><span style="font-size:15px;line-height:20px">Regards</span></font></span></div>
<div><span style="background-color:rgb(255,255,255);text-align:left"><font face="'Trebuchet MS', Arial, Helvetica, sans-serif"><span style="font-size:15px;line-height:20px">Vijayan.R</span></font></span></div><div>
<span style="background-color:rgb(255,255,255);text-align:left"><font face="'Trebuchet MS', Arial, Helvetica, sans-serif"><span style="font-size:1.15em;line-height:1.4em"><br></span></font></span></div><div><span style="background-color:rgb(255,255,255);text-align:left"><font face="'Trebuchet MS', Arial, Helvetica, sans-serif"><span style="font-size:1.15em;line-height:1.4em"> </span></font></span></div>
<div> <br><br><div class="gmail_quote">On Sat, Jan 14, 2012 at 10:45 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
Hovakim Grabski wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
Anyone know any ligand- ligand tutorial?<br>
</blockquote>
<br></div>
If there is no receptor, then there is no ligand ;)<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I've been trying to set up a taurine simulation with lysophosphatidylcholines (LPC) with no success.<br>
</blockquote>
<br></div>
Without a description of what you've tried, what hasn't worked, etc then there's not much anyone can suggest. If you've simply got two small molecules you want to simulate together:<br>
<br>
1. Obtain topologies for both species and construct a .top that calls a force field and the small molecule topologies<br>
2. Set up the coordinate file such that the two species are arranged how you'd like them in a single box (done with editconf)<br>
3. Solvate and proceed as you would any other simulated system<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></span></blockquote></div><br></div>