Difference between revisions of "Avogadro"
From Script | Spoken-Tutorial
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'''Avogadro''' is free and open source cross platform application. | '''Avogadro''' is free and open source cross platform application. | ||
| − | It offers a semantic chemical builder and platform for visualization and analysis.It offers an easy-to-use builder and integrated support for downloading from common databases such as '''PubChem''' and the '''Protein Data Bank'''. Default file format for '''Avogadro''' is CML but it supports wide variety of file formats like .pdb, .mol, .cif and others. | + | It offers a semantic chemical builder and platform for visualization and analysis. It offers an easy-to-use builder and integrated support for downloading from common databases such as '''PubChem''' and the '''Protein Data Bank'''. Default file format for '''Avogadro''' is CML but it supports wide variety of file formats like .pdb, .mol, .cif and others. |
Revision as of 12:57, 10 August 2016
Avogadro
Avogadro is free and open source cross platform application. It offers a semantic chemical builder and platform for visualization and analysis. It offers an easy-to-use builder and integrated support for downloading from common databases such as PubChem and the Protein Data Bank. Default file format for Avogadro is CML but it supports wide variety of file formats like .pdb, .mol, .cif and others.
The Spoken Tutorial Effort for Avogadro has being contributed by Madhuri Ganapathi and Dr. Snehalatha Kalliappan.
Basic Level
1. 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
2. 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.
3. 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.
4. 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
5. 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
6. 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
6. File Extensions
- Prepare input files for computational chemistry programmes such as: GAMESS, Gaussian, MOPAC, NWChem etc.
- View Molecular orbitals and calculated IR spectrum using outputfiles generated from GAMESS and Gaussian software.
