[Chimera-users] [chimera-dev] Energy Minimisation Citation
nancy5villa at gmail.com
Mon Mar 28 17:15:20 PDT 2011
Thank you very much for your explanations, I greatly appreciate it.
On Mon, Mar 28, 2011 at 1:47 PM, Elaine Meng <meng at 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:
> 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 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:
> > 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
> > Konrad.
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