[gmx-users] g_lie query
Anirban Ghosh
reach.anirban.ghosh at gmail.com
Tue Dec 28 14:46:36 CET 2010
Thanks a lot Justin for the reply.
Yes I am going through all the relevant literature on LIE.
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?
Thanks a lot again.
Anirban
On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Anirban Ghosh wrote:
>
>> Thanks a lot Justin for the reply.
>> 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?
>>
>
> 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.
>
>
> And why am I getting only a single value of DGbind for all the frames
>> captured in the .edr file?
>>
>>
> 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.
>
> -Justin
>
> Thanks a lot.
>>
>> Anirban
>>
>>
>> On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Anirban Ghosh wrote:
>>
>> Thanks Justin for the reply.
>> 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?
>>
>>
>> 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.
>>
>> 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.
>>
>> -Justin
>>
>> Thanks a lot.
>>
>> Anirban
>> On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>> Anirban Ghosh wrote:
>>
>> Hi ALL,
>>
>> I have run a protein + ligand (dopamine) simulation. Now
>> I want
>> to calculate the free energy of binding using g_lie. But
>> g_lie
>> asks for two values: Elj and Eqq. How or from where can I
>> get
>> these values for my ligand? Also, do I need to run a
>> simulation
>> with only the ligand? And, is there any other way (like
>> MMGBSA
>> in Amber) to calculate the free energy for my simulation?
>> Any
>> suggestion is welcome.
>> Thanks a lot in advance.
>>
>>
>> Go to the literature and understand what information is
>> needed for
>> such a simulation, and then look into the list archives and
>> you'll
>> find dozens of threads about using g_lie.
>>
>> -Justin
>>
>>
>> Regards,
>>
>> Anirban
>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>>
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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