Re: [Open Babel] computing Gasteiger partial charges

[Geoffrey H. <ge...@ge...>]

> I need to calculate the Gasteiger partial charges for a molecule  
> and can't seem to figure out how to actually do that using open babel.

Well, that depends on what you want. If you're trying to develop  
code, you want to look at OBAtom::GetPartialCharge() which will  
calculate Gasteiger charges if no partial charges have been assigned.

If you want to generate partial charges as a user, I suggest  
translating to Sybyl Mol2 format -- which includes partial charges.  
For example:

babel test1.pdb test1.mol2

Then take a look at the last column for each atom, e.g.:
       1 N1          3.5549    0.1065   -0.0000 N.am    1  UNK         
-0.2483
       2 C1          2.8719    1.2685   -0.0000 C.2     1   
UNK         0.2511
       3 C2          1.3611    1.2472    0.0000 C.ar    1   
UNK         0.0456

Cheers,
-Geoff