ADL: WARNING Non-integral total charge

Michele Lunelli efunit at
Thu Mar 6 08:14:38 PST 2008

Hi Maura,

the warning means that the sums of the partial charges of the atoms of your 
ligand is not zero or an integer number as expected. The partial charges are in 
the 11th column of your pdbqt file. To correct this problem, check the correct 
assignment of the Gasteiger charges. In particular check that your ligand have 
all the correct hydrogens as expected (also the non-polar), assign the charges 
(with ADT Edit/Charges/Compute Gasteiger), then you can check the correctness of 
  the assignment with the menu "Edit/Charges/Check total on residues", and then 
merge the non-polar hydrogens.
If the problem persists you can calculate the charges using the PETRA server at and edit manually 
the pdbqt file.


mmooney05 at wrote:
> Hi all,
>       When I launch autodock4 from the command line I get the following 
> error:
> autodock4: ***WARNING! Non-integral total charge (-0.15e) on ligand!***
> What is the significance of this warning and how can I fix the problem? I 
> would be most grateful for any suggesetions regarding this issue, as I saw 
> it on the mailing list, but no solutions were provided.
> Many Thanx,
>            Maura
> ________________________________________________
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