Hi Marcus
Thank you so much for your offer to help. I'm happy to help user document
avogadro when you get to that point. I started trying avogadro 2 because
avogadro 1 was not saving double bonds, and was also not aware that
avogadro 1 had these extension capabilities. I saved the file in CML which
solved both issues - I was able to open the file in avogadro 2 and also the
double bond information that was created in avogadro 1 displayed in
avogadro 2.
Great, thank you for offering guidance. I used avogadro 1 to calculate the
energy at [Energy = 9,515.9 kJ/mol]. The wiki
<http://avogadro.cc/wiki/Extensions_Menu#Calculate_Energy>does not detail
exactly what is meant by this figure. What is the context for the kJ/mol
figure?
Thank you
Tim
On Wed, Nov 9, 2016 at 10:24 AM, Marcus D. Hanwell <
marcus.hanw...@kitware.com> wrote:
> On Tue, Nov 8, 2016 at 12:44 PM, Tim Potter <thetimpot...@gmail.com>
> wrote:
> > Hello
> >
> > I'm very slowly working through making avogadro2 functional to calculate
> > electron density, bond strain, and total energy for a new carbon
> molecule.
>
> Avogadro 1 and 2 provide a method of generating input for quantum
> codes, such as NWChem, Gaussian, MOPAC, etc. They do not do the
> calculation directly, but can read a number of these outputs.
> >
> > It's been a few days now and I've still not gotten the openbabel plugin
> to
> > optimize geometry properly for a simple benzene molecule, nor have I been
> > able to open PDB files that were made in avogadro1. I see a wiki for
> > avogadro1 but there seems to be almost no documentation for avogadro2.
>
> There is sparse documentation, and some features are simply missing at
> this stage. I am working on some updates, and hope to have more merged
> in the near future so that we can make an updated release. At this
> stage knowing a little more about what you are having trouble with
> would be helpful.
>
> I would recommend saving structures from Avogadro 1 as CML, but PDB
> should probably work too. There is not any user documentation at this
> stage, it is something I would like to put some time into once we are
> closer to having a final release - is there a reason you don't simply
> use Avogadro 1 at this stage?
> >
> > I would prefer to hire someone who is experienced with the software and
> can
> > perform at least one of these three calculations with relative ease.
> >
> We can offer help on this list, the company I work for has consulting
> rates but for such a small task I think I could provide some guidance,
> and even write up a post going through the steps as it would be of
> interest to the wider community.
>
> Marcus
>
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