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

[Eric Pettersen]

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

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




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