[Chimera-users] Asymmetric partial charges on symmetric atoms

Eric Pettersen pett at cgl.ucsf.edu
Tue May 31 11:56:42 PDT 2011

Hi Brian,
	Both sqm and mopac are doing a QM charge calculation, which considers  
the overall electronic environment.  The more negatively charged  
carboxylate oxygen is on the "side" of the molecule that has the  
positively-charged guanidinium group which seems to cause some of the  
negative charge to be shifted to that oxygen.  Chopping out the  
guanidinium group results in the carboxylate oxygens being given  
charges that differ by 0.011.
	If I eliminate all other ring substituents, which leaves a much truer  
symmetric environment for the carboxylate oxygens, then sqm computes  
equal charges for the oxygens (mol2 file attached):

       5 C6         23.4850   19.6920   64.8870 C.2       1 BCZ     
       6 O8         22.2660   19.7760   65.0340 O.co2     1 BCZ    
       7 O7         24.2040   20.8120   64.7970 O.co2     1 BCZ    

	I guess the take home is that the asymmetric charges on the  
carboxylate oxygens is actually the expected behavior.  Now, if you  
feel that the charge transfer is unrealistically high you would have  
to take that issue up with the folks on the Amber mailing list -- I  
certainly don't have the expertise to make those kinds of changes!  Or  
if you felt that Chimera should be invoking sqm with something other  
than sqm's default settings, that is something I could offer control  
over at least.  Let me know if that is the case.


-------------- next part --------------
A non-text attachment was scrubbed...
Name: ring.mol2
Type: chemical/x-mol2
Size: 1728 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20110531/8738620e/attachment.bin>
-------------- next part --------------

On May 27, 2011, at 8:48 AM, Brian Fochtman wrote:

> Hi,
> When adding partial charges (AM1-BCC) to small molecules in chimera,  
> we observed that atoms in symmetrical groups are not assigned the  
> same partial charge. Specifically, the two oxygens in a carboxyl  
> group are not assigned the same partial charge. See excerpt from  
> mol2 file below:
> carboxyl:
>      20 C20        23.4850   19.6920   64.8870 C.2        1 BCZ     
> 0.9226
>      21 O21        22.2660   19.7760   65.0340 O.co2     1 BCZ    
> -0.9253
>      22 O22        24.2040   20.8120   64.7970 O.co2     1 BCZ    
> -0.7643
> There is a significant difference in partial charge between the two  
> carboxyl oxygens (0.161).
> This problem was observed in both older (with mopac) and newer (with  
> sqm) versions of chimera.
> The molecule is peramivir from the pdb1L7F crystal structure.   
> Similar problems were observed for other molecules that inhibit  
> Neuraminidase for example those 1L__ pdb structures.
> This problem is also observed when assigning am1bcc charges to the  
> mol2 file using antechamber/sqm directly.
> Best Regards,
> Brian Fochtman,
> Trent Balius,
> Sudipto Mukherjee
> <1l7f.lig.mol2>_______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list