Thanks Justin.<div>Yes I did use PME during the simulations. But still when I process the .edr file with g_energy, it gives both the options...LJ-1-4 and LJ(SR). So if I am not wrong, I should be using the LJ(SR) value as the Elj in the LIE calculation. Right?</div>
<div><br></div><div>Thanks again.</div><div><br></div><div>Anirban</div><div><br><br><div class="gmail_quote">On Tue, Dec 28, 2010 at 11:45 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>
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>
<br>
While calculating the Elj and Eqq values should we consider the short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in <br>
</blockquote>
<br></div>
1-4 interactions are intramolecular, thus should not be relevant to the LIE calculation.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
the .edr file? And for Coulomb also?<br>
Which one should we consider?<br>
</blockquote>
<br></div>
Did you use PME? If so, you can't break down the Coulombic terms entirely.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thanks again.<br>
<br>
Anirban<div class="im"><br>
<br>
<br>
On Tue, Dec 28, 2010 at 11:03 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 a lot Justin for the reply.<br>
Yes I am going through all the relevant literature on LIE.<br>
Actually the lie.xvg file contains the same value of -25.4 for<br>
all the frames. So I am getting a straight line plot. Why is<br>
this happening? Am I missing out something?<br>
<br>
<br>
If the interactions of your ligand and its receptor are stable, then<br>
there may be no change in the energetics. I don't know anything<br>
about your system, so I can't say anything beyond that.<br>
<br>
-Justin<br>
<br>
Thanks a lot again.<br>
<br>
Anirban<br>
<br>
<br>
On Tue, Dec 28, 2010 at 6:24 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>
Thanks a lot Justin for the reply.<br>
So I ran a simulation with my ligand in water for 1 ns<br>
and using<br>
g_energy I calculated the LG-14 and Coulomb-14 values<br>
from the<br>
.edr file. I supplied the average of these two values as<br>
my Elj<br>
and Eqq to g_lie and I got the DGbind as -25.4. Is this the<br>
correct way to do this?<br>
<br>
<br>
Again I would ask you to not rely entirely upon my advice for<br>
this.<br>
I have only examined the LIE method sparingly. My best<br>
answer is,<br>
"probably," but do read the literature on the method to be sure.<br>
<br>
<br>
And why am I getting only a single value of DGbind for<br>
all the<br>
frames captured in the .edr file?<br>
<br>
<br>
The lie.xvg file contains the LIE values as a function of time.<br>
What's printed to the screen is the average value and standard<br>
deviation.<br>
<br>
-Justin<br>
<br>
Thanks a lot.<br>
<br>
Anirban<br>
<br>
<br>
On Mon, Dec 27, 2010 at 11:51 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>
<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>>><br></div></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>><br>
<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>
Thanks Justin for the reply.<br>
I have through the threads about g_lie, but cannot<br>
understand<br>
how to get the values for Elj and Eqq for a particular<br>
ligand.<br>
Like in my case for a system consisting of a beta2AR<br>
protein +<br>
dopamine (ligand) + POPC + water, what should be the<br>
values for<br>
Elj and Eqq?<br>
<br>
<br>
To obtain these (from my limited understanding), you would<br>
have to<br>
run a simulation of your ligand in water, decomposing the<br>
nonbonded<br>
energies between the ligand and solvent into LJ and<br>
Coulombic<br>
components. Those are your values.<br>
<br>
I should also note that simply going through the<br>
archive to<br>
inform<br>
yourself about the LIE method is insufficient. The<br>
original<br>
literature, and several subsequent papers (one at least<br>
within the<br>
last year, IIRC), describes the accuracy of the method and<br>
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>
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<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>>>><br>
<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>><br>
<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>>><br>
<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>><br>
<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)<br>
simulation. Now<br>
I want<br>
to calculate the free energy of binding using<br>
g_lie. But<br>
g_lie<br>
asks for two values: Elj and Eqq. How or from<br>
where can I get<br>
these values for my ligand? Also, do I need<br>
to run a<br>
simulation<br>
with only the ligand? And, is there any<br>
other way<br>
(like<br>
MMGBSA<br>
in Amber) to calculate the free energy for my<br>
simulation? Any<br>
suggestion is welcome.<br>
Thanks a lot in advance.<br>
<br>
<br>
Go to the literature and understand what<br>
information is<br>
needed for<br>
such a simulation, and then look into the list<br>
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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Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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