<div>Thank you very much for your explanations, I greatly appreciate it.</div><div><br></div><div>Nancy</div><div><br></div><br><br><div class="gmail_quote">On Mon, Mar 28, 2011 at 1:47 PM, Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Konrad,<br>
Thanks for the MMTK citation link. The force field information is in the Chimera minimization man page, for example:<br>
<br>
<<a href="http://www.cgl.ucsf.edu/chimera/1.5.3/docs/ContributedSoftware/minimize/minimize.html" target="_blank">http://www.cgl.ucsf.edu/chimera/1.5.3/docs/ContributedSoftware/minimize/minimize.html</a>><br>
<br>
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,<br>
<div class="im">Elaine<br>
----------<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
</div><div><div></div><div class="h5">On Mar 28, 2011, at 10:24 AM, Konrad Hinsen wrote:<br>
<br>
> On 28 Mar, 2011, at 5:26 , Nancy wrote:<br>
><br>
>> 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?<br>
><br>
> The minimization code used by Chimera comes from MMTK, whose reference is this paper:<br>
><br>
> <a href="http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_2000_2" target="_blank">http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_2000_2</a><br>
><br>
> 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.<br>
><br>
> Konrad.<br>
<br>
</div></div></blockquote></div><br>