> I am struggling with the geometry optimization routine "obminimize"
> within Open Babel. It works perfectly, but I wonder how I can put
> the resulting structure back into a *.mol2 file, since the result
> only appears in the command window.
You can redirect output to the terminal, e.g.:
obminimize ... >out.mol2
> 1. Are there already semi-empirical calculation routines for
> geometry optimization available such as AM1 etc.?
No. I highly doubt we will ever implement quantum mechanics inside
Open Babel. People have requested some level of molecular mechanics
for handling conformer searching and 3D coordinate generation (e.g.,
from SMILES or InChI).
If you're looking for semi-empirical QM, I suggest looking at packages
like MOPAC2009.
> 2. Which optimization method should I use, conjugate gradients or
> steepest descent? Both lead to different results.
Ultimately, they should lead to the same minimum geometry, although
not necessarily with the same number of steps. If your geometry is far
from a minimum, steepest descent is probably better than conjugate
gradients. However, the latter is usually faster to converge to a
minimum.
Cheers,
-Geoff
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