[Chimera-users] sulfone files

Eric Pettersen pett at cgl.ucsf.edu
Wed Sep 3 15:02:52 PDT 2008

Hi Barb,
	There are two issues here.  One was that though the heavy-atom  
positions were identical, the added hydrogens weren't positioned  
identically because of "steric clashes" between the two molecules when  
placing hydrogens (this was in some fairly newly-added code).  I  
modified the new code to ignore clashes between sibling submodels  
(other analogous older code was already doing this).  With the  
modified code and with the two PDB files merged so that the molecules  
open into model 0.1 and 0.2, the hydrogens get added identically.
	The other issue is that antechamber only determines charges to  
somewhere around 0.01 accuracy, even with the atoms at identical  
positions.  Now, Chimera is supplying antechamber with identical  
positions, but giving them in a different order between the two  
residues, so that the resulting output isn't identical.  I've modified  
the add-charge code so that it will now present the atoms in the same  
order as they were input -- so the result is that the charges vary  
only minimally now.  Nonetheless, they shouldn't really be perceived  
as more accurate than about +/-0.01 charge units.  You'd probably have  
to ask on the Amber mailing list why this is so and if there is  
anything that can be done or will be done about it.
	These changes will be available in tonight's daily build, which you  
could get tomorrow from www.cgl.ucsf.edu/chimera -- follow the "Daily  
Builds" link.


On Sep 3, 2008, at 6:17 AM, Barb Truitt wrote:

> Eric - Thank you for your help. I find the Chimera list incredibly  
> helpful.
> I've verified that the pdb files have the same coordinates. I also  
> redid the DOCK PREP without any rotation of either molecule and  
> still have different charge assignments. Here are the four files.  
> The carbons that vary the most between the two are the ones in the  
> aromatic ring with a single methoxy group and the ones near the  
> chlorine. I'm also sending an Excel file where I've sorted the atoms  
> based on their coordinates so that I could check the assigned  
> charges. I've color-coded the carbons that vary significantly.
> Barb
> <charge  
> comparison 
> .xls 
> > 
> < 
> SSR149415 
> .pdb><SSR149415_SR4.pdb><SSR149415_SR_T.mol2><SSR149415_T.mol2>

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