Home   Manual

Polymer modeling

Hii all,
I am a newbie to avogadro
Actually I would like to build a polymer of about 350 monomer units. Polymer of interest is polycaprolactone. Using avogadro how this can be done? which tool and how it is done? I tried simple copy-pasting. but it did’nt work.Manually I built a series of 10 monomers, but when i re-open it the bond types changes. Why so ?
please help with this.
Looking forward for your suggestions

Thankyou

Hi! Thanks for your question.

As far as “bond types changing” - this depends on what file format you use for saving. If you save to a format that supports bond orders (e.g., CML, SDF) you’ll have no problem retaining bond orders. If you save to XYZ or PDB, then Avogadro has to guess the connectivity and bond orders again, which might change.

I’ve been building up some polymer tools, but they’ll be added to Avogadro v2, which can better handle large molecules. Generally the easiest way to build a long polymer is through iterative copy/paste

  • build the monomer
  • copy/paste to create the dimer
  • copy/paste the dimer to get a tetramer
  • copy/paste the tetramer to get an octamer
  • repeat …