[gmx-users] Free Energy of Binding Question

Abdülkadir KOÇAK kocak at gtu.edu.tr
Tue Sep 20 15:27:10 CEST 2016

What I am doing is exactly as you said; decoupling the ligand once from the WT and once from the MUT. And now I see that I am getting "absolute" free energies in each case. I did not run MD for the proteins in the absence of the ligand. As you mentioned even for the absolute binding free energies, the value is too high.

I don't know whether you could help answering for that with the .mdp file options used in the production MD step (I attached). I have a Zn2+ containing enzyme with charged ligand. The co-crystal structures for both WT and MUT with ligand are available.

As the protocol, I first energy minimized (in two step 1- steep 2- cg, 5000 total steps) , NVT (200 ps) and NPT (1 ns) equilibrated the systems (For each lamda values of course). Then the equilbrated structures were run 10 ns in final MD... For the decoupling parameters I used the same lambda values in the .mdp for each simulation step.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk>
Sent: Tuesday, September 20, 2016 3:45:51 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Cc: gmx-users at gromacs.org
Subject: Re: [gmx-users] Free Energy of Binding Question

It usually helps to draw a thermodynamic cycle to inform yourself what
exactly you are doing.

What you seem to have been doing is to decouple the ligand, once from
the WT and once from the MUT.  This should give you the "absolute"
binding free energy.  Computing the difference between those values
will give you the relative binding free energy.  It is unclear to me
what exactly you mean with dG=1134 kJ/mol but if this is the absolute
binding free energy it seems to be excessively high.  But without
knowing the details regarding the setup and simulation protocol it will
not be possible to find out what could have gone wrong.

Of course, you could also compute the relative free energy by
transforming WT to MUT, once in presence of the ligand and once without
the ligand (side-chain mutation). Principally, both approaches should
give you comparable results.

On Tue, 20 Sep 2016 11:48:21 +0000
Abdülkadir KOÇAK <kocak at gtu.edu.tr> wrote:

> Dear GMX Community,
> I am aiming to compare the relative binding energy (BE) of a ligand
> to wild type (WT) vs mutant (MUT) protein and thus trying to run a
> Free Energy Calculation for the binding energy of the ligand to both
> proteins (WT and MUT) using Bennett Acceptance Ratio (BAR).
> As the first step, I calculated decoupling of the ligand from both
> proteins in two seperate MD runs by first turning off the coulombic
> interaction and then the van der waals interaction. The next step
> would be the solvation free energies of the ligand in order to get
> the correct BE. However, the ligand is the same for both WT and MUT,
> so in terms of getting relative BE, should we still calculate the
> ligand in water or will the ligand solv energies will cancel in the
> Besides, from the decoupling of the Protein-ligand complex, I am
> getting very high DG values (1134 kJ/mol). Is this meaningful or not?
> Thx

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