Thanks a lot Justin for the reply.<div>So I ran a simulation with my ligand in water for 1 ns and using g_energy I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied the average of these two values as my Elj and Eqq to g_lie and I got the DGbind as -25.4. Is this the correct way to do this? And why am I getting only a single value of DGbind for all the frames captured in the .edr file?</div>
<div><br></div><div>Thanks a lot.</div><div><br></div><div>Anirban<br><br><div class="gmail_quote">On Mon, Dec 27, 2010 at 11:51 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>
Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks Justin for the reply.<br>
I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq?<br>
<br>
</blockquote>
<br></div>
To obtain these (from my limited understanding), you would have to run a simulation of your ligand in water, decomposing the nonbonded energies between the ligand and solvent into LJ and Coulombic components. Those are your values.<br>
<br>
I should also note that simply going through the archive to inform yourself about the LIE method is insufficient. The original literature, and several subsequent papers (one at least within the last year, IIRC), describes the accuracy of the method and what it needs to be properly run.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks a lot.<br>
<br>
Anirban <br><div class="im">
On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Anirban Ghosh wrote:<br>
<br>
Hi ALL,<br>
<br>
I have run a protein + ligand (dopamine) simulation. Now I want<br>
to calculate the free energy of binding using g_lie. But g_lie<br>
asks for two values: Elj and Eqq. How or from where can I get<br>
these values for my ligand? Also, do I need to run a simulation<br>
with only the ligand? And, is there any other way (like MMGBSA<br>
in Amber) to calculate the free energy for my simulation? Any<br>
suggestion is welcome.<br>
Thanks a lot in advance.<br>
<br>
<br>
Go to the literature and understand what information is needed for<br>
such a simulation, and then look into the list archives and you'll<br>
find dozens of threads about using g_lie.<br>
<br>
-Justin<br>
<br>
<br>
Regards,<br>
<br>
Anirban<br>
<br>
<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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