You can set the charges of each atom by choosing "Atom Properties ..." under the View menu. In the Formal Charge column just type the charge for each atom. This might be inconvenient for a large molecule.
You can optimize the geometry by choosing "Optimize Geometry" under the Extensions menu. If you get an error, you might try changing the Force Field by selecting Molecular Mechanics under the Extensions menu.
I have never used Gaussian, so I can't tell you much about how to use Gaussian, but it looks like you can prepare a Gaussian input file from Avogadro by selecting "Gaussian ..." under the extensions menu. Make whatever changes you need and click the "Generate" button to save the Gaussian input file. You will have to run Gaussian next.
I hope this helps,
Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
From: maryam golbabaee [maryamgolbabaee@...]
Sent: Friday, October 26, 2012 3:49 AM
Subject: [Avogadro-Discuss] please do me a favour, answer my question
i am a new user of avogadro. i want to konw how we could put charge on a molecule in avogadro and in big melcule such as rhodamine's ( rhodamine chloride) , how i can use gaussian09,because of optimze geometry,that means i want to konw first of all how i could estimate optimized geometry and afterwards how to run in gaussian09?