|Posted on Monday, April 22, 2002 - 10:26 am: |
The builder seems to have a problem with the molecule: 1,4-Pentadiyne.
The graphic of the molecule (in the builder window (after cleanup)) looks fine ("V-shaped, C_2v), but the Z-Matrix produced has the two "middle" H's superimposed (and so a quick mopac job dies).
Specifying cartesians prevents the superimposed H's but the resulting structure is clearly distorted.
There are two jobs on the demo server which illustrate these problems.
|Posted on Monday, April 22, 2002 - 1:34 pm: |
Unfortunately, since the molecule contains 4 co-linear atoms, it cannot be specified (easily) in terms of a z-matrix because the dihedral angle would be undefined. This explains the presence of the superimposed H's when specifying the geometry in terms of a z-matrix.
As you tried, the correct solution to this dilema is to use cartesian coordinates. Unfortunately, the public domain version of Mopac that we are using on the demo server does not seem to work with cartesian coordiantes (even though the documentation states it does!). It is possible that other versions of Mopac 7 out there DO support cartesian coordiates.
Note that, of course, cartesian coordiantes are supported Mopac 93/2000.