Dear Amber users,
I am working with MD simulations of a protein, which get activated by
divalent ion binding. Many biophysical studies says that the protein I am
working with has multiple ion binding sites. But, unfortunately, none of
such ion binding site has been identified through any structural studies.
The overall objective of my study is to identity such ion binding sites
through extensive all-atom MD simulation of protein in water box with
desired concentration of ions.
Here, I just wondering whether the equilibrium MD simulation of all-atom
systems will able to show the plausible ion-binding sites in the protein?
or do I have to use any biased MD tools like accelerated MD or steered MD
to achieve my objectives?
Any suggestion will be highly appreciated.
Many thanks in advance
Regards
Anu
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Received on Mon Feb 23 2015 - 04:30:02 PST
