[gmx-users] Ligand-Protein interaction with energy groups

Justin Lemkul jalemkul at vt.edu
Wed Sep 19 19:49:43 CEST 2012

On 9/19/12 11:47 AM, 이종화 wrote:
> Greetings all,
> I am trying to compare the stability of two protein-ligand systems where
> ligands differ. I am trying to observe the difference of interaction energy
> between the ligands. Would it be correct to make energy groups of Protein,
> Solvent, Ligand, and compare the energy obtainable by g_energy? I am
> confused because in one tutorial I do also have to run simulation with only
> the ligand and solvents.

You can certainly measure interaction energy in this way, though there are 
probably more robust methods like LIE and free energy calculations.

> If it were to be correct, would comparing the sum of the LJ-14:Protein-LIG
> and Coul-14:Protein-LIG of each ligand be okay?

Neither of those terms will be of any use, and should actually be zero.  1-4 
interactions are intramolecular.  What you're likely more interested in are the 
LJ-SR and Coul-SR terms, though there are still some flaws with doing that, 
especially if using PME.  This topic is discussed frequently on the mailing 
list; the archive should provide many useful discussions on such topics.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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