[Chimera-users] Calculating partial charges of a charged ligand
pett at cgl.ucsf.edu
Thu Mar 15 17:16:44 PDT 2012
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).
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,
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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