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From: David A. Case <case.scripps.edu>

Date: Wed, 26 Dec 2007 09:52:20 -0800

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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Received on Sun Dec 30 2007 - 06:07:06 PST

Date: Wed, 26 Dec 2007 09:52:20 -0800

On Wed, Oct 24, 2007, Catein Catherine wrote:

Sorry to be so very slow in replying -- it took me a long time to get

motivated to look at such an old paper.

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.

Sorry: the question confuses me. The average velocity at the top of the

barrier *is* in Eq. 5, (right after the "1/2").

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.

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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Received on Sun Dec 30 2007 - 06:07:06 PST

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