AMBER Archive (2008)

Subject: AMBER: PMF calculation for binding constant or rate constant?

From: Catein Catherine (
Date: Tue Apr 15 2008 - 21:26:46 CDT

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? Why?
Please kindly help and many thanks in advanced,
News, entertainment and everything you care about at Get it now!
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to