Dear Amber Users,
I have a query that I am trying to simulate a protein kinase where chloride
ion binding site is there. Chloride is making important interactions with
various residues.
I would like to study, if I replace the ion chloride with other ions like
bromide or iodide ion in that pocket and its impact on the interactions
with various residues of the pocket.
I did a cmd simulation by keeping bromide ion, which is already present in
the crystal structure in that pocket, and also checked with chloride. But
upon simulation both bromide and chloride ions move away.
So I don't know how to keep it and study the simulation. How to constraint
it? How to study such systems?
Any suggestions would be highly appreciated.
Thanks and regards
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Received on Sat Oct 03 2020 - 20:00:03 PDT
