Hi Ondrej, It may be possible, but it is not easy and requires editing unfriendly files in somewhat obscure locations in the Chimera installation. I have not tried it myself. For details, see the bottom of the "Minimize Structure" page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h...> I see there is already an element definition file for Fe in the MMTK directory mentioned in those instructions, so I believe it would just require editing the Amber parameter files. I also see there is FE in the top part of parm10.dat, for example, but a second numerical value is missing there, and FE is entirely missing from the RE section at the end of that file. Other possibilities, which may not be what you want: (a) you could ignore the ion entirely using "fragment true" with the "minimize" command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html#fragment> (b) you could change the element of the ion to one that can be handled (say Mg++ or Zn++) although that would use parameters different from what you might use for iron I hope this helps, 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 Oct 17, 2012, at 2:14 AM, Ondřej Holas wrote:
Greetings, I have encountered this problem with energy minimization of pyrazinamidase molecule. This molecule contains within its structure iron atom which Chimera does not support. Therefore I cannot find the way to overcome this problem. Is there any way to add iron to supported elements or any other way to solve this?
Best regards