Thank you very much for your explanations, I greatly appreciate it. Nancy On Mon, Mar 28, 2011 at 1:47 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

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/mini...

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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 ---------- 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:

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On 28 Mar, 2011, at 5:26 , Nancy wrote:

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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

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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.

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Konrad.