Re: [AMBER] Counter Ions in X-Ray structure.

From: David Case <>
Date: Thu, 27 Sep 2018 12:53:16 +0000

On Thu, Sep 27, 2018, Keiran Corbett wrote:

> 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.

Amber should recognize these MG ions, assuming that you have sourced a
leaprc.water.xxxx file in your tleap input. If you are seeing problems, we
would need to know details: esp. is this a "standard" pdb file from the PDB
website? Or might it be a file with non-standard atom or residue names?


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Received on Thu Sep 27 2018 - 06:00:03 PDT
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