Hi Konrad,
Thanks for the MMTK citation link.  The force field information is in the Chimera minimization man page, for example:

<http://www.cgl.ucsf.edu/chimera/1.5.3/docs/ContributedSoftware/minimize/minimize.html>

To summarize, Amber ff99 is used for standard residues and monatomic ions, Antechamber/GAFF for nonstandard residues.   Of course, the page above also mentions MMTK and links to its documentation.  Best,

Elaine
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Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 28, 2011, at 10:24 AM, Konrad Hinsen wrote:

> On 28 Mar, 2011, at 5:26 , Nancy wrote:
>
>> I used the "Minimize Structure" feature of Chimera to minimize several ligand molecules in preparation for docking (with the "Gasteiger" charges option).  I need to cite this in an article that I am to submit for publication, and I need a bibliography of the software, including a description of the minimisation algorithm, force field, etc...  Please let me know how I should go about this?
>
> The minimization code used by Chimera comes from MMTK, whose reference is this paper:
>
>       http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_2000_2
>
> The force field is some dialect of Amber, though I don't know which one exactly is used by Chimera. I hope someone else can provide that information.
>
> Konrad.