[Chimera-users] Minimize and solvate with a zinc ion

Eric Pettersen pett at cgl.ucsf.edu
Fri Jun 12 11:14:04 PDT 2009

Hi JD,
	You can basically ignore that warning and continue on.
	The Solvate tool is still a little rough around the edges.  If you  
have existing ions/solvent when you run Solvate, it looks at the  
charges Amber gave to the added ions/solvent and tries to transfer  
those to the pre-existing ions/solvent.  Since you didn't add any zinc  
ions (naturally), it couldn't -- so it popped up that panel saying  
so.  No real issue for you.  I've now changed the code to suppress the  
panel if the "pre-existing ions" are not alkali metals or halides.

                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Jun 12, 2009, at 2:53 AM, Dr. Jean-Didier Maréchal wrote:

> Dear all,
> I want to solvate then minimize (few steps) a structure with a zinc  
> (Zn2+) ion.
> From what I saw in the manual, zinc parameters are available in the  
> actual version of the amber force field in chimera. However, I am  
> stuck with troubles. When I solvate I have the following message:
> Could not determine charges for pre-existing solvent from added  
> solvent for: Zn Zn
> What do I do wrong?
> All the best,
> JD

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