[Chimera-users] binding energy calculation?

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 29 12:30:32 PST 2009

Hi Ram,
The total energy of the system before minimization and at each update  
is reported in the Reply Log (under Favorites menu).

However, the purpose of the minimization tool is to clean up bad local  
geometries (strains and clashes) -- the energy values are not useful  
for quantitative analyses. They are only potential energies, not free  
energies (they do not include full solvation effects, sampling, or  
entropies) and the minimization only goes toward a local minimum  
rather than finding a global minimum.

Chimera does not do free energy calculations.  You would need to use  
some other program for those more computationally intensive studies.

I hope this helps,
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 Dec 29, 2009, at 8:26 AM, r n wrote:

> hi
> I wanted to do energy minimization for the pdb file with two chains  
> by keeping their backbone fixed , tried
> chimera energy minimization but did not give me any energy after the  
> minization or binding energy for the complex.
> Is it anyway that I could do simulation of side chains and obtain  
> the energy values such as lowest minima or the binding energy for  
> two chains, using chimera?
> thanks
> ram

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