[gmx-users] Problem in Free Energy Calculations

[Justin Lemkul]

On 1/4/16 1:09 AM, shagun krishna wrote:
> Hi Justin,
> You mean to say that I don't need to follow your Free Energy Calculations :
> Methane in Water.
> Actually I want to calculate the binding energy of my ligands with my
> protein. All I should do is to run the one simulation of my ligands simply
> in water and another is the protein-ligand complex simulation, both for
> 10ns. I am really very confused because I have gone through literature and
> all of them have calculated the value of α, β and  γ, which i guess can be
> calculated by using free energy codes.
>

I don't use the LIE algorithm, so I don't know all the details.  AFAIK these are 
empirical parameters to weight various contributions to the interaction energy. 
  LIE is ultimately an estimate of the free energy, and its accuracy depends on 
the quality of the fitted parameters.

A rigorous free energy calculation is the best method for calculating free 
energy of binding.  For instance, LIE (again, AFAIK) relies solely on enthalpic 
terms, so it does not account for entropy unless you do additional work to 
figure this out separately.

-Justin

-- 
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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

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