ADL: How to assign total charge for small molecule

Michele Lunelli efunit at
Thu Feb 14 12:16:27 PST 2008

Dear Tomek,

thank you for your suggestion, the PETRA server is very useful, because I don't 
have access to other programs like InsightII that can calculate Gasteiger charges.
I have also to use total charges like you, because when I calculate sigma 
charges the sum of them on the whole molecule is -0.5, for some reason not clear 
to me (I guess because the other -0.5 is given by pi charges).


Michele Lunelli

Tomek Wlodarski wrote:
> Hi Michele,
> I had similar problem with calculating Gasteiger charges in Autodock, so I
> used PETRA - online server which calculate
> Gasteiger charges - it is run by prof. Gasteiger group so I believe charges
> are calculated very well :) You can chose sigma charges - which are
> calculated in AD and Total charges, I used Total because I had pi-electron
> systems.
> It is free server, and you can build ligand in Java browser - so you can be
> sure that additional negative or positive charges would be on right atom :)
> After that you have to manually edit your pdbqt file and add proper charges
> from PETRA.
> I hope this would help you :)
> Best,
> Tomek Wlodarski

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