Avogadro Procedure

Avogadro

1. After doing these steps for all the molecules you wanted to create then open the program Avogadro.
2. Go to “File” and “Open” to bring a molecule you created in ChemSketch to Avogadro. Find your molecule that you want to bring to Avogadro and select it to open it. Click “Yes” when a small window pops up about 3D coordinates and a rough sketch.
3. Once the molecule is on Avogadro then go to “Extensions” and select “Optimize geometry.”
4. * There is another way to Optimize Geometry How do we do it again???
5. Save the file as “Sybyl Mol2 (*.mol2)”
6. Exit Avogadro.