Molecular Dynamics- Search for conformeres- output file?

Hello everybody!

I’d like to do conformational search with Avogadro and do further work
with the output file. My problem is that I can’t get the output file.
I only can see the results as pictures when I choose a confermer under
"view/properties/confomer properties" and the cartesian coordinates
under “structure/cartesian coordinates editor”

You would help me a lot if you could tell me how to get the files with
the cartesian coordinates for every conformer. If you have a hint how
to eliminate conformers that are doubled in the list this would be
wonderful, too.

Thanks a lot,
Laura

On Mon, 17 Oct 2011 15:46:03 +0100, Laura Wollny laurawollny@googlemail.com wrote:

Hello everybody!

I’d like to do conformational search with Avogadro and do further work
with the output file. My problem is that I can’t get the output file.
I only can see the results as pictures when I choose a confermer under
"view/properties/confomer properties" and the cartesian coordinates
under “structure/cartesian coordinates editor”

You would help me a lot if you could tell me how to get the files with
the cartesian coordinates for every conformer. If you have a hint how
to eliminate conformers that are doubled in the list this would be
wonderful, too.

I’ve not used this much, so I don’t know whether there’s a better way to do it, but one possible option is simply to use Select All, click one of the conformer labels, then Copy and paste the XYZ coordinate set produced into a new Avogadro window or text editor or some such, click the next conformer, copy/paste again, etc. This obviously might not be practical for you if you have a lot of conformers.

-Ian Kirker

On Oct 17, 2011, at 1:35 PM, Ian Kirker wrote:

I’ve not used this much, so I don’t know whether there’s a better way to do it,

Right. The other approach is to click on each of the conformer labels one by one, and choose “File -> Save As” to give a new name.

A colleague asked me for a more automated way to do this a few weeks ago, so I’ll definitely add a more streamlined approach (also for vibrational distortions) in the next few weeks.

-Geoff