[Chimera-users] assignment of charges

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