On Tue, 29 Nov 2011 18:51:22 -0000, Geoffrey Hutchison email@example.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.