[Chimera-users] Energy Minimisation Citation

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 28 09:06:36 PDT 2011

Hi Nancy,
Chimera uses MMTK.  All the information we have is in the "Minimize Structure" manual page, which you can see by starting that tool and clicking the Help button.  If you need more details than are given in that page, you may need to follow the links from that page to the MMTK documentation.

Your ligands are probably "nonstandard residues" as described in that page, and thus GAFF force field parameters as assigned by Antechamber were used.  There are literature citations for both of those in the page.

We also have copies of the documentation on our web site, but I don't know what version of Chimera you are using.  The Help button approach above will open the local copy that goes with what you downloaded.  

I hope this helps,
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 27, 2011, at 8:26 PM, Nancy wrote:

> Dear All,
> 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?
> Thank you very much,
> Nancy

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