AMBER Archive (2007)

Subject: RE: AMBER: Polarizable Force Field: Ligand Parameterization et al.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri Oct 26 2007 - 02:17:16 CDT

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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