Atomic charge in mol2 file

General Discussion Documentation
1

I can’t find the document on how the program assign the partial charge for each atom in a molecule. How do they get those charges? If there is some documentation about that, where can I find it? Thank you very much. I am simply converting from pdb to mol2 file using avogadro.

2

In this case, Avogadro is using Open Babel to save to mol2 format. If you have not already assigned partial charges with Avogadro2, it will default to the Gasteiger charges. Open Babel should actually note that in the file, e.g.

@<TRIPOS>MOLECULE
*****
 14 14 0 0 0
SMALL
GASTEIGER
[…]
3

Thank you very much!!