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

From: David Mobley <>
Date: Wed, 24 Oct 2007 07:20:43 -0700

Dear Catein,

You might want to look at some more recent literature as a starting
point. 19 years is an awfully long time in computational terms.

Best wishes,

On 10/24/07, Catein Catherine <> wrote:
> Dear Prof. Case and other researchers,
> 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.
> (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?
> (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.
> (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.
> (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?
> Sorry to have asked so many questions, I hope you could not mind to give
> me a hand and teach me what should I do next? Thank you very much in
> advanced.
> Best regards
> Cat
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Received on Sun Oct 28 2007 - 06:07:08 PDT
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