Atomic charges on each atom

Hello
Is there any way to see the value of the atomic charges on each atom of the molecule displayed as gaussview?

Thanks in advance

Víctor E. Bahamonde Padilla
Laboratorio Fisicoquimica Molecular
Departamento de Química
Facultad de Ciencias
Universidad de Chile
Phone: 562-978-7443
veduardo@ug.uchile.cl

On Fri, Nov 25, 2011 at 8:46 AM, Victor Eduardo Bahamonde Padilla
victorb@live.cl wrote:

Hello
Is there any way to see the value of the atomic charges on each atom of the
molecule displayed as gaussview?

Click “Display Settings” and check “Label”, then open the label
configuration dialog. In Atom Labels --> Text there are Formal Charge
and Partial Charge options. However, I don’t see an way to set the
formal charges, other than to read them in from a calculation or enter
them manually under View --> Properties --> Atom Properties.

Does anyone know of a way to perceive them? This sounds like something
OpenBabel should be able do.

Dave

On Fri, 25 Nov 2011 18:09:03 -0000, David Lonie loniedavid@gmail.com wrote:

On Fri, Nov 25, 2011 at 8:46 AM, Victor Eduardo Bahamonde Padilla
victorb@live.cl wrote:

Hello
Is there any way to see the value of the atomic charges on each atom of the
molecule displayed as gaussview?

Click “Display Settings” and check “Label”, then open the label
configuration dialog. In Atom Labels --> Text there are Formal Charge
and Partial Charge options. However, I don’t see an way to set the
formal charges, other than to read them in from a calculation or enter
them manually under View --> Properties --> Atom Properties.

Does anyone know of a way to perceive them? This sounds like something
OpenBabel should be able do.

As far as I can tell from the OpenBabel source, it should read (Mulliken) charges from .log files but not from formatted checkpoint files. Charge information is contained in both, but the fchk format reader doesn’t seem to contain any code to read it in from fchks as far as I saw.

So, I guess the answer for now is: open the .log file instead of the .fchk file, if you haven’t already. I gave it a quick try using Avogadro 1.1.0 and it seems to work, though as an additional note, Victor, you may have to add the Label display if it’s not already in the list of display types, by clicking “Add” (the one next to “Duplicate” and “Remove”), then selecting “Label”, “OK”, then following the procedure above to set it to show partial charge labels.

(I can’t help thinking this is a thing that could stand to be a bit easier/more intuitive to do. Maybe some sort of “Add Labels…” option under the View menu?)

-Ian

On Fri, Nov 25, 2011 at 1:52 PM, Ian Kirker ian.kirker@gmail.com wrote:

On Fri, 25 Nov 2011 18:09:03 -0000, David Lonie loniedavid@gmail.com wrote:

On Fri, Nov 25, 2011 at 8:46 AM, Victor Eduardo Bahamonde Padilla
victorb@live.cl wrote:

Hello
Is there any way to see the value of the atomic charges on each atom of the
molecule displayed as gaussview?

Click “Display Settings” and check “Label”, then open the label
configuration dialog. In Atom Labels --> Text there are Formal Charge
and Partial Charge options. However, I don’t see an way to set the
formal charges, other than to read them in from a calculation or enter
them manually under View --> Properties --> Atom Properties.

Does anyone know of a way to perceive them? This sounds like something
OpenBabel should be able do.

As far as I can tell from the OpenBabel source, it should read (Mulliken) charges from .log files but not from formatted checkpoint files. Charge information is contained in both, but the fchk format reader doesn’t seem to contain any code to read it in from fchks as far as I saw.

I think OpenBabel has an algorithm somewhere (OBAtomTyper maybe?) that
should be able to perceive formal charges from new molecules built by
hand, too. But I’m not sure if this is exposed in Avogadro or not. I
can’t find anything after a quick check.

So, I guess the answer for now is: open the .log file instead of the .fchk file, if you haven’t already. I gave it a quick try using Avogadro 1.1.0 and it seems to work, though as an additional note, Victor, you may have to add the Label display if it’s not already in the list of display types, by clicking “Add” (the one next to “Duplicate” and “Remove”), then selecting “Label”, “OK”, then following the procedure above to set it to show partial charge labels.

Yes – thanks for pointing this out :slight_smile:

(I can’t help thinking this is a thing that could stand to be a bit easier/more intuitive to do. Maybe some sort of “Add Labels…” option under the View menu?)

The current design is aimed at modularity so that new display types
can be added easily, and I agree, the interface ends up being rather
opaque from a new user’s viewpoint. Your suggestion is a good one,
however, the current library design doesn’t allow for display engines
to provide menu actions. I think that improving menu/action/feature
customizability should be a focus for 2.0 – after all, that is the
major benefit of the modular approach :wink:

Dave

On Nov 25, 2011, at 1:52 PM, Ian Kirker wrote:

As far as I can tell from the OpenBabel source, it should read (Mulliken) charges from .log files but not from formatted checkpoint files. Charge information is contained in both, but the fchk format reader doesn’t seem to contain any code to read it in from fchks as far as I saw.

If you can point me to the sections of the fchk which contain partial charges, I’m happy to add them – it’s really easy. (For example, do ESP or other formal charges show up in the fchk?)

(I can’t help thinking this is a thing that could stand to be a bit easier/more intuitive to do. Maybe some sort of “Add Labels…” option under the View menu?)

That’s a good suggestion. I’ve long had a ToDo item to add a “Hide Hydrogens” option under the view menu too. Sadly, right now, it’s too many features, not enough time. Fortunately, more help is coming soon.

-Geoff

On Tue, 29 Nov 2011 18:51:22 -0000, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

On Nov 25, 2011, at 1:52 PM, Ian Kirker wrote:

As far as I can tell from the OpenBabel source, it should read (Mulliken) charges from .log files but not from formatted checkpoint files. Charge information is contained in both, but the fchk format reader doesn’t seem to contain any code to read it in from fchks as far as I saw.

If you can point me to the sections of the fchk which contain partial charges, I’m happy to add them – it’s really easy. (For example, do ESP or other formal charges show up in the fchk?)

I’m using g09_a02, just in case it’s different between g03 and g09 or subversions.

So, using for example a water calculation (it’s always water), in a QM calculation there are (always, as far as I can tell) Mulliken charges:
Mulliken Charges R N= 3
-6.32265630E-01 3.16132815E-01 3.16132815E-01

If you add “pop=npa” to the route line, you can also get NPA charges in there:
NPA Charges R N= 3
-9.53490152E-01 4.76745076E-01 4.76745076E-01

And, similarly, “pop=esp”, ESP charges:
ESP Charges R N= 3
-7.46505199E-01 3.73252600E-01 3.73252600E-01

Adding in the calculation of Hirshfeld charges seems to only add those to the logfile, not the fchk, alas.

I don’t think it does contain formal charge, but it does contain information on the number of bonds to each atom and connectivity - I can run some quick tests to see what this is based on (e.g. what you specify, or some automatic bond-finder, and whether it counts doubles as two) if this’d be useful.

-Ian