[gmx-users] g_lie query

[Justin A. Lemkul]

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

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