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

Eric Pettersen pett at cgl.ucsf.edu
Thu Mar 15 17:16:44 PDT 2012

Hi Christos,
	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.
	I'm sorry I don't have anything more useful to offer (except to  
suggest using AM1-BCC charges instead).


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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 at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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