Hi Alec, Chimera uses MMTK to do the minimization. After some investigation last month (since others asked the same question), we concluded that MMTK does not provide an energy breakdown, sorry. A little more perspective on the "Minimize Structure" tool: It is one of the cruder or "early phase of development" features in Chimera. Currently it affords very little control over the force field parameters and other parameters (cutoffs, minimization algorithm, etc.) and is not particularly efficient (partly due to lack of cutoffs). I would view this tool as a convenient but rough way to clean up localized strains and clashes, but not as a replacement for a full-featured minimization/simulation package such as Amber or Charmm. How it works and some discussion of the limitations can be found in the man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 25, 2007, at 8:17 AM, Alec Zander wrote:
Hello! New to the software and this list. Looks great!
I minimized a structure, and I'm seeing the changes afterwards. However, I also want to see an output file with a detailed energy report on the stability and what terms contributed how much, like at the end of a CHARMM run (which is what I've used almost exclusively till now). Any pointers?
Thanks,
Alec _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users