[Chimera-users] Gasteiger charge

Eric Pettersen pett at cgl.ucsf.edu
Thu Oct 13 15:11:07 PDT 2011

On Oct 13, 2011, at 1:29 PM, Ibrahim Moustafa wrote:

> Dear Chimera developers:
>   I want to assign Gasteiger charges for a ligand, as a preparative  
> step for docking.  The ligand is GTP, extracted from a protein  
> complex structure.
>   I wanted to add the Gasteiger partial charge, and explicitly chose  
> to have a total charge of “-4” on the ligand molecule.  However, the  
> program assigned partial charges that sum to total charge of “-2”  
> instead of “-4”.
>   Any idea why the program assigned the Gasteiger partial charges  
> incorrectly, ignoring the input total charge on the ligand.

Amber's antechamber program (which Chimera uses for charge assignment)  
does not honor the '-nc' flag (net charge) for Gasteiger charges.  It  
just uses what it believes the charge to be, which I guess in this  
case is -2 (weird choice!).  You can see complaints about this if you  
google for "gasteiger" along with "nc".

If you use the latest daily build (tomorrow's!) then you can use AM1- 
BCC charges for GTP.  We've added "charge templates" for GTP/GDP/ADP/ 
ATP since antechamber frequently fails with highly negatively-charged  
systems, so we used charges taken from the Amber parameter database  
for those commonplace residues.  However, in constructing the template  
for GTP I missed HO3', so that's why you would need to get tomorrow's  

Finally, you should probably use AddH separately and see if Chimera  
adds a proton to the terminal phosphate of your GTP.  If it does,  
delete it before adding charges.  The template charges are for GTPs  
with no protonation on the terminal phosphate.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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