On May 3, 2010, at 7:01 PM, abdullah ahmed wrote:

I wish I could use a picture :)
Unfortunately, this is not possible since I need the energy value to be able to compare this to other mutations of the same structure and to provide a "measure" of how energetically favourable one is in comparison to the other.
Ok, that is what I was suspecting ... then you should be really careful in using the minimized energy as a "measure" of the different effect of the mutations in protein. This has probably
not much value!
You'd need to go to the free energy and not the enthalpy (potential energy) of one minimized frame

And I am using a box of water because I feel that provides a better estimation of natural conditions than a vaccum :)
In that case I am afraid the water should be relaxed ... equilibrated if you prefer. Its interaction with the protein is probably no-sense. A minimization is not
sufficient to fix it.




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