[gmx-users] binding delta G, H and S for ion-protein

[Justin Lemkul]

On 3/16/14, 11:48 AM, Andrew Bostick wrote:
> Dear groamcs users
>
>
> I want to calculate binding delta G.
>
> I know g_lie tool is used to calculate delta G for protein-ligand or
> enzyme-drug binding.
>
> Can I use g_lie tool o calculate delta G for binding some ions to one
> protein molecule?
>

LIE is not just used for ligands and drugs.  It can apply to anything that binds 
to anything else, provided its underlying assumptions hold.

>
> Generally, which toolS of gromacs are appropriate for delta G, delta S and
> delta H for binding some ions to one protein molecule?
>

What you're asking to do is a free energy calculation.  Many different methods 
might apply - PMF, TI, FEP, BAR, etc.  See the manual and available tutorials.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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