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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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