On Oct 5, 2011, at 4:31 AM, green69 wrote:

> Please, does anybody know if there is a way to calculate the partial charges
> independently from those of input file?

The command you used would generate Gasteiger charges. If the input file 
already has Gasteiger charges, the result will be the same. If you want 
different charges, try a different charge model, like MMFF94, r QEq.

Hope that helps,
-Geoff
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