[gmx-users] g_lie query

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 17 13:26:26 CEST 2010

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.


> Regards,
> Anirban


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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