Thanks a lot Justin for the reply.<div>Yes I am going through all the relevant literature on LIE.</div><div>Actually the lie.xvg file contains the same value of -25.4 for all the frames. So I am getting a straight line plot. Why is this happening? Am I missing out something?</div>
<div><br></div><div>Thanks a lot again.</div><div><br></div><div>Anirban</div><div><br><br><div class="gmail_quote">On Tue, Dec 28, 2010 at 6:24 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 a lot Justin for the reply.<br>
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? <br>
</blockquote>
<br></div>
Again I would ask you to not rely entirely upon my advice for this. I have only examined the LIE method sparingly. My best answer is, "probably," but do read the literature on the method to be sure.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
And why am I getting only a single value of DGbind for all the frames captured in the .edr file?<br>
<br>
</blockquote>
<br></div>
The lie.xvg file contains the LIE values as a function of time. What's printed to the screen is the average value and standard deviation.<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<div class="im"><br>
<br>
On Mon, Dec 27, 2010 at 11:51 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>
Thanks Justin for the reply.<br>
I have through the threads about g_lie, but cannot understand<br>
how to get the values for Elj and Eqq for a particular ligand.<br>
Like in my case for a system consisting of a beta2AR protein +<br>
dopamine (ligand) + POPC + water, what should be the values for<br>
Elj and Eqq?<br>
<br>
<br>
To obtain these (from my limited understanding), you would have to<br>
run a simulation of your ligand in water, decomposing the nonbonded<br>
energies between the ligand and solvent into LJ and Coulombic<br>
components. Those are your values.<br>
<br>
I should also note that simply going through the archive to inform<br>
yourself about the LIE method is insufficient. The original<br>
literature, and several subsequent papers (one at least within the<br>
last year, IIRC), describes the accuracy of the method and what it<br>
needs to be properly run.<br>
<br>
-Justin<br>
<br>
Thanks a lot.<br>
<br>
Anirban<br>
On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul<br>
<<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>><br></div><div><div></div><div class="h5">
<mailto:<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<br>
I want<br>
to calculate the free energy of binding using g_lie. But<br>
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<br>
simulation<br>
with only the ligand? And, is there any other way (like<br>
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<br>
needed for<br>
such a simulation, and then look into the list archives and<br>
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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Virginia Tech<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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