LES can't be easily used to study rates. you can use it to identify possible
paths. at that point you might need something like umbrella sampling or a
path sampling tool to study the free energy profile for moving along the
path and the relative affinities at different sites.
On Wed, Sep 1, 2010 at 2:13 AM, Computational Chemist <
computationalchemist.ymail.com> wrote:
> Dear Amber users,
>
> I have been studying the probability of presence of oxygen binding pocket
> in a
> dioxygenase enzyme . The pocket has not been verified by the crystal
> structure.
> I used MD simulation and LES in this study. The oxygen copy/copies remained
> within 1A from the binding pocket for 50-100 ps, then started leaking out .
> How
> long should the oxygen remain in the proposed binding pocket to verify its
> presence?. All the literature I have read so far were studying the gas
> diffusion
> pathways not the gas biding pocket.
>
> Other Two questions related to MD analysis:
>
> 1- I need to plot the probabilty of oxygen molecules within 1A of the
> pocket
> against time. How should I calculate the probability?
>
> 2- How should I locate the center of mass of the oxygen copies?
>
>
> Thank you,
> Darine
>
>
>
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Received on Wed Sep 01 2010 - 07:30:04 PDT
