Generate Z-matrix coordinate file.

When I use Gaussian to scan bond, angle or dihedral, I need to use Z-matrix coordinate. I have two ways to do this.

  1. Use AMBERTOOLS with command
    antechamber -i 1.pdb -fi pdb -o 1.gzmat -fo gzmat
  2. Use Avogadro to open the structure file. Choose Extensions–Gaussian. and choose “z-matrix” in format option.

I have checked the output of the two method. Only numbering of atoms are the same, the values of bond, angle or dihedral have a very very slight difference that I think could be ignored.

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