[ghemical-devel] Exporting from GChemPaint to Ghemical

[Tommi Hassinen]

On Tue, 29 Jun 2004, Jean Br=E9fort wrote:

> > But averaging the coordinates should do the centering trick.
> >
>
> Thanks, it works. I must now try to transfer as far as possible the
> stereochemistry (not so simple). At the moment, when I transfer a
> molecule such as cholesterol with all z coordinates set at 0., I cannot
> optimize the geometry (nan values everywhere). More simple molecules
> work. Have a nice summer.

Hummm... I guess the calculations fail because there is something bad in
the initial geometry. It might be some of the following:

1) some atoms (most likely H and non-H atoms?) have identical coordinates
(or otherwise overlap badly), creating bonds with zero length.

2) some bond angles have extreme values of 0.0 deg or 180.0 deg.

The problems above cause computations to fail because there are some
infinite or undefined intermediate values (that is, for example a division
by zero can happen in the calculations).

How you could avoid this, is to modify the structure (even randomly!) a
bit if the structure contains some errors mentioned above. Even a tiny
modification is often enough to make the calculations work again.

Have a nice summer,

=09Tommi