[Chimera-users] Calculating partial charges of a charged ligand

Christos Deligkaris deligkaris at gmail.com
Thu Mar 15 08:17:28 PDT 2012

Dear Chimera users,

I have a charged ligand (formal charge of +2) and I have tried using
Chimera to calculate the partial charges of that molecule.

Even though Chimera predicts correctly that the net charge is +2, after
calculating the partial charges (using the Gasteiger method) I see that the
sum of all partial charges is zero.

Changing the net charge of the molecule seems to have no effect on the
calculation of the partial charges.

It also seems that the Gasteiger website does not offer the service of
calculating the partial charges any more... (

Do you have any suggestions on how to calculate the Gasteiger charges so
that the net charge on my molecule is +2?

Thank you for your help,

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