On Apr 18, 2014, at 10:05 AM, Elaine Meng <meng@cgl.ucsf.EDU> wrote:

The calculation of charges for nonstandard residues is done by the Antechamber package included with Chimera, rather than Chimera directly. I'm guessing that small (e.g. 0.001) deviations from integer total charges are fairly common and are caused by rounding of the per-atom values.

Exactly. Chimera uses Antechamber by sending it a Mol2 file as input and reading its output, which is also a Mol2 file. The charges for the atoms in the Mol2 file are three decimal places and therefore due to roundoff their sum may be non-integral, differing in the third decimal place.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu