[Chimera-users] minimization with nonstandard atoms

Jon N. Rumbley jrumbley at d.umn.edu
Tue Feb 7 09:00:45 PST 2012

I was hoping to minimize a homology model containing two heme groups. To
understand how I might do this I have been starting with the known structure
1a6m. As suggested in the documentation I begin with Dock Prep and calculate
charges etc. To my surprise Chimera alpha version 1.6 (build 34702) actually
assigned charges to the heme. The problem is with the minimization itself.
Within Minimize Structure I turn off all of the Dock Prep steps and simply
try to minimize the structure but get an error,"Element Fe (atom
#0:154.A at FE) is not currently supported". I was assuming the charge calc was
going to be the hard part but now I am stuck at this subsequent step. Is
there something I can do to get the heme atoms recognized or is this simply
not possible?


Thank you,

Jon Rumbley


Dr. Jon N. Rumbley

Assistant Professor

Dept. of Pharmacy Practice and

Pharmaceutical Sciences

University of Minnesota-Duluth

127 Life Sciences

1110 Kirby Dr.

Duluth, MN 55812

Phone: 218-726-6047

email: jrumbley at d.umn.edu



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120207/4e9839cb/attachment.html>

More information about the Chimera-users mailing list