I think we need to spend some time working on default force-fields.
Most users don’t know UFF from MMFF94 and will see errors like allene
and blame Avogadro (not the force field).
Cheers,
-Geoff
Begin forwarded message:
From: xis19+@pitt.edu
Date: September 7, 2008 11:15:17 PM EDT
Subject: A user report of AvogadroDear Prof. Hutchison,
I have been looked for a organic molecule draw tool in Linux/KDE for a
long time, and your Avogadro really impressed me a lot. It seems used
quantum chemistry calculation to optimize the structure of the
molecule,
and it works very well for me. However, I found a few (possible)
bugs. One
of them is, I tried to draw CH_2=C=CH_2, and the result is a flat
molecule: all atoms are in one plane. It is impossible as two \pi
bonds
are perpendicular. Another problem is, I also tried several inorganic
molecule, and the result is not good, sometimes even ridiculous. My
personal interest is organic and do not have plenty of computational
chemistry knowledge, but I do hope the program can be improved.
Furthermore, I myself hope Avogadro can help me draw organic
structures
like ChemDraw. I have some Qt/C++ programming skills but I do not have
sufficient time.Best wishes
Xiaoge Su