> After I solvated my protein, I used "addIons" to add ions to the
> system to reach certain ion concentration. I found that some ions were
> placed outside of the water box. Is this normal? When I used AMBER8
> long time ago, this did not happen. I was wondering if this is
> something with the new version of AmberTools.
I wonder how big the water box is. Addions uses a grid based on
a given distance from the solute, and a small box might fall
within that distance.
Bill
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Received on Fri Jul 22 2011 - 14:00:05 PDT
