Difference between revisions of "Avogadro"
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| − | The Spoken Tutorial Effort for Avogadro has being contributed by Madhuri Ganapathi and Dr. Snehalatha Kaliappan | + | The Spoken Tutorial Effort for Avogadro has being contributed by Madhuri Ganapathi and Dr. Snehalatha Kaliappan''' |
| + | '''Learners''': UG/PG Chemistry and Bioinformatics students. | ||
| + | |||
| + | https://script.spoken-tutorial.org/skins/common/images/button_bold.png | ||
__TOC__ | __TOC__ | ||
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==Basic Level== | ==Basic Level== | ||
| − | '''1. Build Molecules''' | + | '''1. Overview of Avogadro''' |
| + | |||
| + | * About Avogadro software | ||
| + | * Download and installation of Avogadro in Windows OS | ||
| + | * Download and installation of Avogadro in Mac OSX | ||
| + | * Download and installation of Avogadro in Ubuntu Linux | ||
| + | * Open documentation page | ||
| + | * About Avogadro interface and menus | ||
| + | * Explain the benefits of Avogadro | ||
| + | * Play the video clippings of the tutorial series on the Spoken Tutorial website | ||
| + | |||
| + | '''2. Build Molecules''' | ||
* Import Molecules from chemical database | * Import Molecules from chemical database | ||
| Line 30: | Line 44: | ||
* Build DNA/RNA molecules and peptides | * Build DNA/RNA molecules and peptides | ||
| − | ''' | + | '''3. Edit Molecules''' |
* Add and delete atoms | * Add and delete atoms | ||
| Line 38: | Line 52: | ||
* Copy, paste and join structures. | * Copy, paste and join structures. | ||
| − | ''' | + | '''4. Create Surfaces''' |
* View properties of the molecule | * View properties of the molecule | ||
| Line 45: | Line 59: | ||
* Color the surface according to the electrostatic potential energies. | * Color the surface according to the electrostatic potential energies. | ||
| − | ''' | + | '''5. Hydrogen Bonding''' |
* How to configure Avogadro | * How to configure Avogadro | ||
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| − | ''' | + | '''1. General Features in Avogadro''' |
| + | |||
* Proton transfer in compounds by changing pH values | * Proton transfer in compounds by changing pH values | ||
* Load crystal structures from Crystal library | * Load crystal structures from Crystal library | ||
| Line 66: | Line 81: | ||
* Build carbon nano tubes | * Build carbon nano tubes | ||
| − | ''' | + | '''2. Stereoisomerism''' |
| + | |||
* Define stereoisomerism | * Define stereoisomerism | ||
* Define conformational isomerism | * Define conformational isomerism | ||
| Line 78: | Line 94: | ||
==Advanced Level== | ==Advanced Level== | ||
| − | ''' | + | '''1. File Extensions''' |
| + | |||
* Prepare input files for computational chemistry programmes such as: GAMESS, Gaussian, MOPAC, NWChem etc. | * Prepare input files for computational chemistry programmes such as: GAMESS, Gaussian, MOPAC, NWChem etc. | ||
| − | * View Molecular orbitals and calculated IR spectrum using | + | * View Molecular orbitals and calculated IR spectrum using output files generated from GAMESS and Gaussian software. |
Latest revision as of 12:33, 18 November 2019
Avogadro
Avogadro is a free and open source, advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc.
Avogadro has features for high quality rendering, interactive tools, commands and powerful plug-in architecture. The features also include easy import of chemical files from Open Babel, multiple computational packages, crystals and biomolecules.
It is easy to install and source code is available under GNU GPL.
The Spoken Tutorial Effort for Avogadro has being contributed by Madhuri Ganapathi and Dr. Snehalatha Kaliappan
Learners: UG/PG Chemistry and Bioinformatics students.
https://script.spoken-tutorial.org/skins/common/images/button_bold.png
Basic Level
1. Overview of Avogadro
- About Avogadro software
- Download and installation of Avogadro in Windows OS
- Download and installation of Avogadro in Mac OSX
- Download and installation of Avogadro in Ubuntu Linux
- Open documentation page
- About Avogadro interface and menus
- Explain the benefits of Avogadro
- Play the video clippings of the tutorial series on the Spoken Tutorial website
2. Build Molecules
- Import Molecules from chemical database
- Rotate the molecules
- Zoom in and zoom out the structures
- Build molecules on the Panel using Draw tool
- Set up force field and optimize the geometry using optimization tool
- Measure bond lengths, bond angles and dihedral angles
- Show fragment library
- Build DNA/RNA molecules and peptides
3. Edit Molecules
- Add and delete atoms
- Add and delete bonds
- Rotate bonds and change length of the bond
- Change hydrogen to methyl group
- Copy, paste and join structures.
4. Create Surfaces
- View properties of the molecule
- Label the atoms with partial charge
- Create Van der waals surface
- Color the surface according to the electrostatic potential energies.
5. Hydrogen Bonding
- How to configure Avogadro
- Show Intermolecular hydrogen bonding
- Show Intramolecular hydrogen bonding
- Measure length of hydrogen bonds
- Show Force display type in water molecules
- Show dipole moments in molecules
Intermediate Level
1. General Features in Avogadro
- Proton transfer in compounds by changing pH values
- Load crystal structures from Crystal library
- Explain about Miller indices and planes
- Show various Miller planes in crystal systems
- Build super cell in three dimensions
- Show geometries in coordination compounds
- Build carbon nano tubes
2. Stereoisomerism
- Define stereoisomerism
- Define conformational isomerism
- Show conformations of 1,2-dichloroethane
- Show conformations of cyclohexane
- Define geometrical isomerism
- Demonstrate geomertical isomerism
- Explain R S configuration priority rules
- Demonstrate R-S configurations with examples
Advanced Level
1. File Extensions
- Prepare input files for computational chemistry programmes such as: GAMESS, Gaussian, MOPAC, NWChem etc.
- View Molecular orbitals and calculated IR spectrum using output files generated from GAMESS and Gaussian software.
