[gmx-users] Energy difference - Gromacs, Autodock

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 14 21:10:55 CEST 2007

Александр Журавлев wrote:
> Hello Gromacs users! Let me ask you a questions about comparison of energy values resulted from Autodock ligand-receptor docking and Gromacs MD stimulation. 
> The middle potential energy of ligand-receptor interaction (Gromacs, 1000 psec MD stimulation) is about 65 kcal/mol. This seems to be a common case, as PE and Coul energies of different ligands interaction with homologous subtypes of receptor are in the order of 50 - 100 kcal/mol. However the total energy of ligand-receptor interaction after docking to the same position is in the range of 7-15 kcal/mol for different ligands (Autodock 3.0, literature data). All of them contain a carboxylic group that interacts with a positive charged Arg side chain group within the binding pocket of receptor. 
> Can't these huge energy differences be connected with the incorrectly low value of dielectric permeability ε during MD stimulation, maybe due to the incomplete water saturation of binding pocket? 
> Is it a correct way of Gromacs energy units translation to kcal/mol - simply to divide energy value by 4,18?
> Thank you!
4.184 is correct. The value that autodock gives is a binding free 
energy, so entropy comes into play as well. How did you compute the 65 
kcal/mol? You have to subtract ligand/solvent energies, as in the LIE 
approach to be able to compare.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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