AMBER Archive (2007)

Subject: Re: AMBER: Potential of mean force, how to calculate rate of dissociation?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu May 03 2007 - 21:13:55 CDT

Dear David and Jerome,

Thank you very much for your help! Could you mind to let me know how to do
the WHAM, is it a module of AMBER, or another software?

Cat

>From: "David Mobley" <dmobley_at_gmail.com>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: Potential of mean force, how to calculate rate of
>dissociation?
>Date: Thu, 3 May 2007 15:17:31 -0700
>
>Hi,
>
>>Could you please kindly help me? Can I do the potential of mean force
>>calculation with AMBER? Can I calculate the rate of dissociation of a
>>drug
>>from the binding site? If yes, could you mind to give me some hints how
>>to
>>do so with AMBER?
>
>The other user who answered your mail is on the right track.
>
>But I should also point out that a potential of mean force will not
>give you a dissociation rate. It will give you an equilibrium
>dissociation constant (or a dissociation free energy, which is
>related). If you want a dissociation rate, you'll have to look
>elsewhere (experiment?).
>
>David
>
>
>>Best regards,
>>
>>Cat
>>
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