I have counter ions i.e. Mg2+ in the binding site of my protein-ligand
strucuture determined by X-ray crystallography.
I wondered what people thought was the best way to deal with this as AMBER
doesn't recognise these kind of counter ions.
And simply deleting the Mg2+, would I think, affect the answer to my
calculations too much.
(Which is an MD followed by MM/GBSA)
Many thanks
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Received on Thu Sep 27 2018 - 05:00:03 PDT
