Re: [Avogadro-Discuss] paid modeling work and/or tutor

[Geoffrey Hutchison]

> Great, thank you for offering guidance.  I used avogadro 1 to calculate the 
> energy at [Energy = 9,515.9 kJ/mol].  The wiki does not detail exactly what 
> is meant by this figure.  What is the context for the kJ/mol figure?

This depends on what force field you used (likely UFF). It’s a relative energy 
that, in principal, corresponds to a heat of formation. Force field energies 
are not terribly reliable.

-Geoff
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Re: [Avogadro-Discuss] paid modeling work and/or tutor

[Marcus D. Hanwell]

On Thu, Nov 10, 2016 at 12:34 PM, Tim Potter  wrote:
> 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.

I am glad this helped, CML saves bonding information whereas PDB has
only limited support.
>
> Great, thank you for offering guidance.  I used avogadro 1 to calculate the
> energy at [Energy = 9,515.9 kJ/mol].  The wiki does not detail exactly what
> is meant by this figure.  What is the context for the kJ/mol figure?
>
I think that is the energy calculated by Open Babel using a molecular
mechanics force field. You would need to use an input generator, and
run a quantum code if you wanted to get a more accurate number (that
would also be slower in general).

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Re: [Avogadro-Discuss] paid modeling work and/or tutor

[Tim Potter]

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
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 
> 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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> Training and support from Colfax.
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Re: [Avogadro-Discuss] paid modeling work and/or tutor

[Marcus D. Hanwell]

On Tue, Nov 8, 2016 at 12:44 PM, Tim Potter  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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