Cartesian to internal coordinates (z-matrix representation)

Question

[cossio]

What tools are available to go from cartesian coordinaes (in PDB format) to internal coordinates (Z-matrix) representation, where the dihedral angles match actual rotable torsion angles in the molecule?

So far I've seen that Molden can do this, but it has a terrible interface and I don't know how to script it. Moreover, I don't have a way to keep track of which atoms in the original PDB numbering correspond to which atoms in the Z-matrix returned by Molden. This is something I need.

Also desirable is that the Z-matrix follows as closely as possible the bonding of the molecule. That is, an atom's internal coordinates should be defined in terms of atoms to which it is connected through the bonding network.

Answer 1

[João Rodrigues]

Have a look at OpenBabel: http://openbabel.org/wiki/Babel#File_Formats