[Chimera-users] [chimera-dev] Energy Minimisation Citation

[Nancy]

Thank you very much for your explanations, I greatly appreciate it.

Nancy



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:
>
> <
> 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
> ----------
> 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.
>
>
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