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

[Justin Lemkul]

On 1/6/16 12:52 PM, shagun krishna wrote:
> 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.

I was pointing it out for clarity in the archive only; I know you understand 
this point, but when someone types in the right words to Google, they may get 
seriously confused by what they see :)

> 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. *

1-4 interactions are intramolecular terms. These are not what you want.

You need:

(1) Protein-ligand interaction energy (from energygrps = Protein LIG) in the 
complex simulation. You pass this .edr file to gmx lie.  Of course, if water 
plays any role in the interaction of the protein, or it is partially hydrated in 
the binding site, the result you get will not be right.
(2) Ligand-water interaction energy (from energygrps = LIG SOL) from a 
simulation of the ligand in water. You pass these values to -Eqq and -Elj to gmx 
lie.

As for the -Clj and -Cqq values, I still don't know.  Hopefully someone who does 
will chime in with something useful.  But again, the primary literature (and 
there are a number of LIE papers, I'm just not well-versed in their details) 
should tell you everything you need.

-Justin

> *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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-- 
==================================================

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

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