[Chimera-users] post minimization energy report?

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 25 09:16:13 PDT 2007

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:

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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
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