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

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

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

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