Avogadro is changing bonds from saved file

Hello, I’m a newbie at Avogadro. I drew a molecule derived from an amino
acid, optimized its geometry with Avogadro, saved the file and closed it.
But then when I opened it briefly later some bonds were changed. Actually
this is happening all the time with the same bonds (single bonds in a
benzene ring are being converted to double ones and vice-versa). I just want
to keep the molecule as I draw it. Could someone please tell me how I will
be able to do this?

On Sep 21, 2011, at 10:48 AM, George Barbosa wrote:

Hello, I’m a newbie at Avogadro. I drew a molecule derived from an amino acid, optimized its geometry with Avogadro, saved the file and closed it. But then when I opened it briefly later some bonds were changed

Depending on the file format you used, bonding information may not be included. Avogadro uses CML as its native format, which will store bond orders. But if you save as a PDB or XYZ format, bond orders are not saved and Avogadro will have to work out the bond orders again.

Also, keep in mind that Avogadro attempts to re-center a molecule when opening – this may rotate the frame of reference so that atoms are not in the same place.

Hope that helps,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/