

AMBER Archive (2007)Subject: AMBER: How to calculate the timedependent transmission coefficient for rate constant esimation from PMF ca From: Catein Catherine (askamber23_at_hotmail.com)Date: Fri Oct 26 2007  02:28:57 CDT
Dear Sir/Madam, Could you please kindly teach me how to use AMBER to calculate rate constant for a proteinligand 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 timedependent 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.
 
