Re: [chimera-dev] [Chimera-users] Energy Minimisation Citation
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. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research AT khinsen DOT fastmail DOT net ---------------------------------------------------------------------
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.
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...
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.
participants (3)
-
Elaine Meng -
Konrad Hinsen -
Nancy