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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