Avogadro Procedure: Difference between revisions

From Rasulev Lab Wiki
Jump to navigation Jump to search
(Imported from text file)
 
m (Revised formatting)
 
Line 1: Line 1:
__TOC__
__TOC__


Avogadro:
====== Avogadro ======
 
# After doing these steps for all the molecules you wanted to create then open the program Avogadro.
# After doing these steps for all the molecules you wanted to create then open the program Avogadro.
# 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.
# 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.
Line 8: Line 7:
# * There is another way to Optimize Geometry How do we do it again???
# * There is another way to Optimize Geometry How do we do it again???
# Save the file as “Sybyl Mol2 (*.mol2)”
# Save the file as “Sybyl Mol2 (*.mol2)”
# Exit Avogadro.
# Exit Avogadro.<br />
 
<br />
<br />

Latest revision as of 20:55, 26 September 2022

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.