Solution LAB2 guanine

• Back to the previous page: Electronic properties of isolated molecules#Exercise1

Step 1

• Once you have Avogadro installed, open it and let's use the molecular builder to visualise a Guanine molecule:

Build --> Insert-->Fragment-->nucleobases-->guanine

Click on the selection settings "arrow" and right click to visualise the molecule.

Clicking on manipulate settings "hand" you can then rotate the molecule.

• Now we perform a classical relaxation using an Avogadro built-in Force Filed

Extension-->Molecular Mechanics and we choose a FF

Extension-->Optimize geometry

In few steps we have our relaxed geometry that we can save in .xyz format using:

File-->Save as-->select .xyz format and save in your disk as guanine_FF.xyz

Step 2

Now we are ready to perform a QM relaxation. As a first step, update your pseudo potentials directory by using git commands:

git pull

new pseudo potentials (Nitrogen and Oxygen) will be downloaded in your pseudo potential directory.