Is there a command line way (Linux or Windows) to open a structure of a certain molecule in the Avogadro (.mol file, for example), change a specific bond length of this molecule and generate a zmatrix (Gaussian input, for example)?
I would like to do it several times.
Thanks in advance.
I am not aware of a possible way to use Avogadro in scripts. It’s a GUI app. I guess you will need to use something else for z-matrix preparation, maybe OpenBabel.