[gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach

[Justin Lemkul]

On 1/6/16 1:20 AM, shagun krishna wrote:
> Dear Gmx-user,
>
> I am using LIE approach to calculate the binding energy of my protein and
> ligand. When I am running g_lie program for my protein I am getting the
> value of DeltaG= 0. Can you please suggest me a way to get the values of
> Elj, Eqq, Clj and Cqq and also about the post-processing necessary to run a
> LIE calculation. It is not given in tutorial. I have ran two separate
> simulations: one for receptor-ligand complex and another for ligand alone
> in solvent.  I am following Justin tutorial for free energy calculation.
>

For the sake of clarity in the archive, I again reiterate that my free energy 
tutorial has nothing to do with LIE.

The values of Elj and Eqq are what you get from simulating the ligand in water 
with appropriate energygrps.

The values of Clj and Cqq are the parameters you have to figure out.  What do 
the papers on LIE say?  There are defaults given in gmx lie, where do they come 
from?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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