[gmx-users] g_lie query

[Justin A. Lemkul]

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

========================================