[gmx-users] Energy difference - Gromacs, Autodock

Александр Журавлев beneor at mail.ru
Thu Jun 14 14:21:13 CEST 2007

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!

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