[gmx-users] g_lie query
Anirban Ghosh
reach.anirban.ghosh at gmail.com
Tue Dec 28 19:21:53 CET 2010
Thanks Justin.
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?
Thanks again.
Anirban
On Tue, Dec 28, 2010 at 11:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Anirban Ghosh wrote:
>
>> Thanks a lot Justin for the reply !!!
>>
>> 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
>>
>
> 1-4 interactions are intramolecular, thus should not be relevant to the LIE
> calculation.
>
>
> the .edr file? And for Coulomb also?
>> Which one should we consider?
>>
>
> Did you use PME? If so, you can't break down the Coulombic terms entirely.
>
> -Justin
>
>
>> Thanks again.
>>
>> Anirban
>>
>>
>>
>> On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Anirban Ghosh wrote:
>>
>> 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?
>>
>>
>> If the interactions of your ligand and its receptor are stable, then
>> there may be no change in the energetics. I don't know anything
>> about your system, so I can't say anything beyond that.
>>
>> -Justin
>>
>> Thanks a lot again.
>>
>> Anirban
>>
>>
>> On Tue, Dec 28, 2010 at 6:24 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:
>>
>> 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>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto: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>>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> <mailto: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> <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> <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> <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
>
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