[Chimera-users] assignment of charges

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 2 13:32:11 PDT 2008

Are the coordinates identical?  Antechamber/Mopac only produces  
identical charges if the absolute coordinates are identical.  Keep in  
mind that rotating/translating the molecule in Chimera before adding  
charges will change the absolute coordinates.  As for why Antechamber/ 
Mopac is like that, you would have to ask on the Amber mailing list:   
The Amber Molecular Dynamics Package

If you believe the coordinates are identical, make sure that Chimera  
is determining the element types correctly (Actions->Label->element).   
If still no difference, send me the files to look at!


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Aug 29, 2008, at 6:06 AM, Barb Truitt wrote:

> I have two different pdb files that differ only in how the atoms are
> listed in the atom name columns. In one file all of the Carbon atoms
> are listed simply as C. In the other file, the carbon atoms are
> numbered C1, C2, etc. This is true for the other atoms in the
> molecule, which is not a peptide chain. The mol2 files created by
> Chimera under the dock prep procedure have different charges assigned
> to the atoms, differing most in the aromatic carbons. Some of the
> hydrogens also have different charges assigned to them. Most of the
> differences are small, but some are 10%. What is the explanation for  
> this?
> Barb Truitt
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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