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 Tue Aug 31 2010 - 23:30:03 PDT
