Here is an .xyz file of CO2:
======================
3
CO2
C 0.000 0.000 0.000
O 0.000 0.000 1.180
O 0.000 0.000 -1.180
======================
When I use the USPEX online Zmatrix convertor, it gives the correct results:
=========================================
Atom Bond-length Bond-angle Torsion-angle i j k
(Angstrom) (Degree) (Degree)
O 0.0000 0.0000 0.0000 0 0 0
C 1.1800 0.0000 0.0000 1 0 0
O 1.1800 180.0000 -0.0000 2 1 0
==========================================
MOL_name
Number of atoms: 3
O 0.0000 0.0000 -1.1800 0 0 0 1
C 0.0000 0.0000 0.0000 1 0 0 1
O 0.0000 0.0000 1.1800 2 1 0 1
==========================================
While the Zmatrix2 convertor gives the wrong ones:
=========================================
Atom Bond-length Bond-angle Torsion-angle i j k
(Angstrom) (Degree) (Degree)
O 0.0000 0.0000 0.0000 0 0 0
C 1.1800 0.0000 0.0000 1 0 0
O 1.1800 180.0000 nan 2 1 0
O 0.0000 nan nan 1 2 3
=========================================
MOL_name
Number of Atoms: 4
O -1.1800 0.0000 0.0000 0 0 0 0
C 0.0000 0.0000 0.0000 1 0 0 0
O 1.1800 0.0000 0.0000 2 1 0 0
O -1.1800 0.0000 0.0000 1 2 3 0
=========================================
The most serious one is that USPEX program read it wrong so that it generated no structures with correct molecular shape and couldn't run correctly:
=========================================
The calculated Zmatrix is:
Atom Bond-length Bond-angle Torsion-angle i j k
(Angstrom) (Degree) (Degree)
O -1.1803 0.0000 0.0000 0 0 0
C 1.1803 90.0000 0.0000 1 0 0
O 1.1803 180.0000 NaN 2 1 0
=========================================
How can I fix it or somehow bypass this?