[gmx-users] g_lie query

[Anirban Ghosh]

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? And why am I getting
only a single value of DGbind for all the frames captured in the .edr file?

Thanks a lot.

Anirban

On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul <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>> 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> | (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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