AMBER Archive (2007)

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

• Next message: francesco zonta: "AMBER: HG atoms in CYX residues"
• Previous message: Catein Catherine: "AMBER: Average absolute value of cross velocity (Rate constant from PMF)"
• In reply to: Yong Duan: "RE: AMBER: Polarizable Force Field: Ligand Parameterization et al."
• Next in thread: cgji: "Re: Re: AMBER: AMBER 9 - Force Field Options - Question"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

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.
_________________________________________________________________
News, entertainment and everything you care about at Live.com. Get it now!
http://www.live.com/getstarted.aspx
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

• Next message: francesco zonta: "AMBER: HG atoms in CYX residues"
• Previous message: Catein Catherine: "AMBER: Average absolute value of cross velocity (Rate constant from PMF)"
• In reply to: Yong Duan: "RE: AMBER: Polarizable Force Field: Ligand Parameterization et al."
• Next in thread: cgji: "Re: Re: AMBER: AMBER 9 - Force Field Options - Question"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]