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Help me to develop PEG Structure

Hey there, I am a high school graduate from India and currently I am invested in an internship at IIT Delhi(One of India’s most reputed STEM Universities) regarding Computational Materials Science. I am just getting started with the subject and I’m pretty much a novice. I’m tasked with the development of Sucrose’s structure and pdb file and Polyethylene Glycol (40 - mer) structure using Avogadro. I am done with the Sucrose task, and I am able to develop a single unit of PEG. However, developing 39 more of these manually feels like a very arduous task. Can anyone help me out, as how can I make it more easily?

Great! Remember that Avogadro allows copy-and-paste. If you’ve made one repeat:

Great, now you have two units. Save a copy.

  • Copy / paste and slide over and you’ll have 4 repeats.
  • Select None and draw the new connection between the carbon and the oxygen atom

Your screen should look something like this:

Save a copy.

  • Copy and paste again, etc. and you’ll have 8 units. Save.
  • Copy and paste again, and you’ll have 16 units. :slight_smile: Save a copy.
  • Copy and paste again, and you’ll have 32 units. Save a copy.

Now you don’t want to go from 32 => 64. Don’t copy this time, you’ll just do another paste (so 32 + 16 = 48).

You can use the select tool + Edit => Clear to remove some extra repeat units.

Now the resulting structure needs some cleanup.

  • Pick the “Auto Optimize” tool and wait. :slight_smile:

Thank you so much, I’ll hope to successfully build the structure with your method.