[gmx-users] g_lie query

[Justin A. Lemkul]

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
> 

-- 
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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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