[Chimera-users] Structure minimization

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 15 09:35:44 PST 2013


Right, it is just standard minimization as described here:

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

"It is intended for cleaning up small molecule structures and improving localized interactions within larger systems. It may not be able to resolve large-scale distortions or widespread structural problems. By definition, energy-minimization simply moves the system toward a local minimimum without crossing energy barriers, and does not search for the global minimum."

On Jan 15, 2013, at 9:31 AM, Bobo Dang wrote:

> Got it, I  submitted a bug report with the pdb file I am working on.
> 
> One more thing, the minimize function in Chimera is just to give a minimized structure in the local environment, it does not cross the energy barrier to give the structure which has the minimum energy of the system, is that right?
> 
> thank you
> 
> bobo




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