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 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