Avogadro
Avogadro is a free, open source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas [1].
Module
List the versions available as modules:
module spider avogadro
Output:
--------------------------
avogadro: avogadro/1.2.0
--------------------------
...
See how to load the version you need:
module spider avogadro/<version>
Load any required modules that are reported by the spider command, and then load the avogadro module:
module load avogadro/<version>
Running
Avogadro is a viewer and thus requires visual access to the HPC cluster. You can start an interactive session with graphical access using methods details under our guide for Graphical Access. Once you session is established, open a terminal and follow the steps in the previous section to load the Avogadro module. Once the module is loaded, follow the steps below to open an example molecule in Avogadro.
Download Example Structure
Download an example molecule (Caffeine) from RCSB:
wget https://files.rcsb.org/ligands/view/CFF_model.sdf
Open Example Structure
Open the Avogadro software with the command:
avogadro
Then go to File->Open and select the file CFF_model.sdf that we previous downloaded. Click "Open" and Avogadro will display the molecule.