Dear Amber users,
I need to identify bridging waters and ions in a protein - ligand simulation (the ligand is parameterized with GAFF). I am not sure how the "bridgeout" keyword works. The manual says it detects bridging solvent molecules, but I don't know if that applies to ions. I need to detect bridging ions, if any, along with bridging water molecules, if any. Also, how exactly is "bridging" defined here?
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Received on Fri Jan 18 2019 - 03:00:03 PST
