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

[shagun krishna]

Thanks for your reply Justin. I know it well that your that tutorial is
nothing to do with g_lie. But being as a gromacs user I am not getting this
point so I am asking this question.
For the protein I am taking all the default values which has been set by
g_lie program. And for the ligand we have to calculate it using g_energy
module. I have done with that part also. But f*or my ligand I am obtaining
Elj (LJ-14)= 226.365 and Eqq (*Coulomb-14) *= -125.048 (both in KJ/mol).**
When I am comparing them with their respective counterpart for the protein
(Clj and Cqq value 0.181 and 0.5 respectively; the Elj and Eqq values are
set 0 for the protein), they seem to be very large. Is it natural or there
is something wrong in my procedure. *
*PS I have performed simple gromacs simulation of ligand in water (that has
not included your free energy codes).*

*Regards*

*Shagun*

On Wed, Jan 6, 2016 at 9:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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