[Chimera-users] assignment of charges

[Barb Truitt]

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