[Chimera-users] adding parameters for minimization

[Elaine Meng]

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.html#limitations>

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