[Chimera-users] Question reagrding potential energy value

[Elaine Meng]

Dear Marie,
I believe the units are kcal/mol and higher is less favorable.

However, for several reasons, these values CANNOT be used to compare  
the stabilities of a wild-type and mutant protein:

- each is only for a local minimum conformation, not the global minimum
- they are not free energies, which would include entropic effects
- they are only comparisons of the folded state and do not include the  
relative stabilities in the unfolded state
- presumably the structures are not solvated

To make statements about the relative stabilities of the proteins, you  
would need to do much more sophisticated calculations (not available  
in Chimera) such as free energy perturbation or thermodynamic  
integration to calculate values along the relevant legs of the free  
energy cycle.  It is beyond the scope of this mailing list to explain  
further!  There should be many descriptions of such approaches in the  
literature, textbooks, and software manuals (AMBER, GROMOS, ...).

The "minimize structure" tool is intended only to clean up local  
strains and conflicts in the structures, not to provide relative  
stabilities.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Feb 2, 2009, at 10:08 AM, Pancera, Marie (NIH/VRC) [E] wrote:

> Hello,
> I am using the minimize structure tool under structure editing.
> I am using this tool because I would like to compare energies for a  
> WT and a mutant structure (point mutant).
> I am getting potential energy value in the reply log.
> I wanted to check with you is there is a unit that I can use for  
> that potential energy.
> I also would like to know if this means that the higher potential  
> energy value means that the protein is less stable.
> Foe example, the potential energy for the WT is: 3132.577437
> The potential energy for the mutant is: 2858.355152
> So that means that the mutant protein has a lower energy and is more  
> stable, right?
> Thanks you,
> Marie
>