When I use Gaussian to scan bond, angle or dihedral, I need to use Z-matrix coordinate. I have two ways to do this.
- Use AMBERTOOLS with command
antechamber -i 1.pdb -fi pdb -o 1.gzmat -fo gzmat
- 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.