Gaussian Z matrices

General Discussion
1

Hello all,

I am trying to create Gaussian Z matrices for my work.

However, there are issues in the output from Avogadro. For example,

H 5 r6 4 a6 1 d6
H 5 r7 4 a7 1 d7
C 5 r8 4 a8 1 d8

atoms 5, 4, and 1 appear 3 times. This means that that torsion cannot be
scanned in Gaussian because it isn’t properly defined.

Open Babel has the same problem when I convert an xyz file from Avoagadro to
gzmat.

Is there a way to get a proper Z matrix?

thanks for your time,
-Dave

2

At the moment, the Avogadro (and Open Babel) code has a heuristic to minimize collinear atoms and 180° dihedrals. If you’d like to suggest another heuristic, we can probably work on it.

Right now, the z-matrix code also won’t create dummy atoms, and this may be needed to reconcile your molecule.

Without seeing the entire molecule (e.g., Cartesian geometry) I don’t have the faintest idea how to solve your problem, other than to put into the code an if/else to look for reuse of angle/dihedral atom definitions.

Alternatively, is there another open source program which gives you a satisfactory z-matrix?

Thanks,
-Geoff

On Aug 29, 2011, at 4:25 PM, David Condon wrote:

Hello all,

I am trying to create Gaussian Z matrices for my work.

However, there are issues in the output from Avogadro. For example,

H 5 r6 4 a6 1 d6
H 5 r7 4 a7 1 d7
C 5 r8 4 a8 1 d8

atoms 5, 4, and 1 appear 3 times. This means that that torsion cannot be scanned in Gaussian because it isn’t properly defined.

Open Babel has the same problem when I convert an xyz file from Avoagadro to gzmat.