Re: question about free energy calculation through FEP method in NAMD

From: Jérôme Hénin (
Date: Wed Jul 14 2021 - 05:31:05 CDT

Hi Maryam,

----- On 14 Juil 21, at 8:35, M. <> wrote:

> Dear Jérôme,
> Hi

> Do you have any suggestions to solve this problem?
> I want to calculate the free energy ( ΔG ) between a ligand and protein through
> FEP method in NAMD. In my structure, the ligand is located on the surface of
> the protein, not inside the protein, lt means a part of the ligand that is
> closed to the protein surface has interaction with protein, and the other part
> of the ligand which is in contact with water molecules, has interaction with
> these molecules. So, when I change the B column of atoms of ligand to -1 (in
> solvate.fep file), the energy (VdW and Elc) turns off for all atoms of ligand
> (all atoms in contact with protein and water molecules both) while I need to
> eliminate the only interaction between the ligand and protein.

Not really. In the double decoupling scheme you need to remove interactions with the solvent as well. Here, you could say that half of the binding site is made of water.

The other branch of double decoupling will let you compare this with the free energy of interaction of the ligand with pure water.

> How can I specify that it eliminates just the interaction between the ligand and
> protein and does not consider the interaction of ligand and water molecules.

That is not implemented, but I don't think it is necessary.


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