AMBER Archive (2007)

Subject: Re: AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 26 2007 - 11:52:20 CST

On Wed, Oct 24, 2007, Catein Catherine wrote:
>
>
> I am reading an article published by Prof. Case in 1988, regardng the use of
> the PMF to calculate the rate constant for a reaction pathway. I am fresh
> to this area, following, I could like to ask for your professional advices,
> please kindly help.

Sorry to be so very slow in replying -- it took me a long time to get
motivated to look at such an old paper.

>
> (1) I noted the average absolute value of the crossing velocity was listed
> in the second column of the Table III. Could you please kindly instruct me
> how to get these numbers from the PMF result?

You can't get an average velocity from a PMF. The method of obtaining the
average velocity is described in Ref. 10 of that paper.
>
> (2) What is the use of average velocity at the top of the barrier and
> equation (6) regarding the reduced masses, as it does not seem to appear in
> equation (5) of the paper for the calculation of kTST.

Sorry: the question confuses me. The average velocity at the top of the
barrier *is* in Eq. 5, (right after the "1/2").

>
> (3) Related to the question (2), I cannot reproduce the kTST listed in the
> fifth column of Table III. I should have missed something very important,
> as I have only time 2.594e4 with 3.737e-10 according to equation (5) of the
> paper.

If I understand you correctly, it looks like you are missing the first term
inside the curly brackets in Eq. 5, the "rho(delta+)" term, which is the same
as exp(-W(delta*)/kT), where W(delta*) is given in Table 3.

>
> (4) I noted some publication find the plateau value of transmission
> coefficient, what additional simulation or calculation should I do the get
> this values done? Is it a must to do this calculation if similar binding
> site and only qualiative discussion would be make?

It is generally not essential for qualitative discussions to estimate the
transmission coefficient. You might want to look at another paper I wrote in
1988(!):

%A D.A. Case
%T Dynamical simulation of rate constants in protein-ligand interactions
%J Prog. Biophys. Molec. Biol.
%V 52
%P 39-70
%D 1988

...again, apologies for taking so long with this....dac

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