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

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

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