[Dock-fans] partial atomic charges in mol2 files in ZINC

John Irwin jji at cgl.ucsf.edu
Fri Oct 21 13:39:52 PDT 2005


Dear DOCK5 / ZINC-mol2 file users
 
    The current version of ZINC contains MMFF94 charges rather than AMSOL
partial atomic charges in the mol2 format files. The next version of ZINC
will have AMSOL partial atomic charges. Until the new version is available,
the workaround is to download mol2 files and run them through a program such
as molcharge, part of OpenEye's QuacPac suite. There are other fine programs
that will assign partial atomic charges. This documentation appears on our
web page: http://blaster.docking.org/rtfm/databases.html
 
Thanks for your interest in DOCK, and ZINC. We hope to have a much improved
version of the database available soon.
 
John
 
 
John J. Irwin http://johnirwin.compbio.ucsf.edu
<http://johnirwin.compbio.ucsf.edu/> 
Adj. Assistant Professor  http://shoichetlab.compbio.ucsf.edu
<http://shoichetlab.compbio.ucsf.edu/> 
Pharmaceutical Chemistry, UCSF, 1700 4th St, Suite 501D
San Francisco CA 94143-2550 USA; Phone +1 415 514-4127 Fax x4260
(For Express Mail please use 94158 as zip)

Free 3D screening database:  <http://zinc.docking.org/>
http://zinc.docking.org. If you are interested in the structure and function
of large molecular assemblies please see the Erice Crystallography page
<http://crystalerice.org/> http://crystalerice.org. Coming soon:
2007: Engineering of Crystalline Materials Properties
2008: From Molecules to Medicine - Integrating Crystallography (Drug Design)
2009: High Pressure Crystallography
2010: Powder Diffraction
2011: Electron Crystallography
 
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