Unfortunately this is an underlying problem of the antechamber program (from AmberTools) that Chimera is using. When computing Gasteiger charges antechamber ignores the charge specified (with the -nc flag) and instead bases the charge on what its estimate of the Gasteiger atoms types of the molecule are. I have complained about this on the Amber mailing list (e.g. http://archive.ambermd.org/201006/0627.html) but so far the behavior remains unchanged. I suggest you complain on the list as well -- the squeaky wheel gets the grease.

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

On Mar 15, 2012, at 8:17 AM, Christos Deligkaris wrote:

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... (http://www2.chemie.uni-erlangen.de/services/petra/smiles.html)

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,

--
Christos
_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users