Dear Chimera users,<br><br>I have a charged ligand (formal charge of +2) and I have tried using Chimera to calculate the partial charges of that molecule.<br><br>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.<br>
<br>Changing the net charge of the molecule seems to have no effect on the calculation of the partial charges.<br><br>It also seems that the Gasteiger website does not offer the service of calculating the partial charges any more... (<a href="http://www2.chemie.uni-erlangen.de/services/petra/smiles.html">http://www2.chemie.uni-erlangen.de/services/petra/smiles.html</a>)<br>
<br>Do you have any suggestions on how to calculate the Gasteiger charges so that the net charge on my molecule is +2?<br><br>Thank you for your help,<br clear="all"><br>-- <br>Christos<br>