Re: [AMBER] detecting bridging waters and ions with cpptraj

From: Daniel Roe <>
Date: Thu, 24 Jan 2019 11:16:07 -0500


A bridging

On Fri, Jan 18, 2019 at 5:48 AM Stefan Ivanov <> wrote:
> 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?

As mentioned in the manual, a bridging water is "solvent that is
hydrogen bonded to two or more different solute residues at the same

You should be able to determine bridging ions by including them in the
'solventdonor' and 'solventacceptor' keywords, e.g.

hbond solventdonor :WAT,Na+ solventacceptor :WAT.O,Na+ ...

Hope this helps,


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Received on Thu Jan 24 2019 - 08:30:02 PST
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