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:
- 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.
- Can I trick Avogadro by editing these files into some modified amino
acids? That would be great! 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.
Thanks and regards,