Question about modifications to the builder library


First of all let me thank the developers for a wonderful software! I am
trying to use the builder module of Avogadro to generate some polypeptide
structures consisting of modified amino acid residues. As a shortcut, I
thought to modify the corresponding .zmat file for the amino acids provided
in the “builder” folder. I had two questions regarding this:

  1. Can you please clarify the format of these .zmat files? These are not
    same the Gaussian Z-matrix format that I am normally familiar with. These
    look similar, but with some extra columns.
  2. Can I trick Avogadro by editing these files into some modified amino
    acids? That would be great! :slight_smile: Please point out if I need to be careful
    about certain requirements, e.g. the atom names/numbering etc necessary for
    the peptide bond formation.

Please advise.

Thanks and regards,
Suman Chakrabarty.