[Chimera-users] Gasteiger charge

[Eric Pettersen]

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  
build.

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


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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