[Chimera-users] adding parameters for minimization
meng at cgl.ucsf.edu
Wed Oct 17 10:29:03 PDT 2012
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:
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
(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 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:
> 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
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