AMBER: PMF calculation for rate constant or binding constant?

From: Catein Catherine <>
Date: Wed, 16 Apr 2008 10:28:43 +0800

Dear Sir/Madam,
I noted from the literature that sometime the result of potential of mean force was used to calculate the rate constant or binding constant of reaction .
I done a Potential of Mean Force calculation for the dissociation of drug from a receptor accords to the binding distance between the active site and the drug. There is not covalent bond between them. I got a contact minima at ~5 A at zero kcal/mol of PMF energy. The free energy profile increase till 10 A at 8 kcal/mol. The free energy level off at 8 kcal/mol after 10 A, which indicate the total removal of drug.
I have difficulty to decide if the I shoud use the 8 kcal/mol to calculate the rate constant or the binding constant, as I cannot see an obvious transition state. It is a must that I should be able to observe a clear transition state by PMF calculation? Could it be affected by the methods that I used or the restrainst used in the umbrella sampling?
I also noticed that some publication rescale the WHAM result to make the level off (in this case is 8 kcal/mol) to zero, while the minimum was set as a negative values (in this case is -8 kcal/mol). Is it necessary to be done?
Please kindly help and many thanks in advanced,
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Received on Fri Apr 18 2008 - 21:19:43 PDT
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