AMBER: How to calculate the time-dependent transmission coefficient for rate constant esimation from PMF ca

From: Catein Catherine <>
Date: Fri, 26 Oct 2007 15:28:57 +0800

Dear Sir/Madam, Could you please kindly teach me how to use AMBER to calculate rate constant for a protein-ligand interaction? My question is becauase of the existence of recrossing, the TST rate constant needs to be corrected by a transmission coeficient, which will necessarily be less than unity. However, how can we derives the time-dependent transmission coefficient by amber? To my understand I may have to do the restraint MD at the TS conformation for a period of time. However, how can I determine the number of recrossing form the result? Or did I misunderstand anything important? Please kindly help. Best regards, Cat.
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Received on Sun Oct 28 2007 - 06:07:32 PDT
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