Minimize and solvate with a zinc ion
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 *************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es
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
participants (2)
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Dr. Jean-Didier Maréchal -
Eric Pettersen