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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