On May 3, 2010, at 6:40 PM, abdullah ahmed wrote:
Actually I'd just like to know why both structures have such similar
coloumb energy values.
If an electro-static interaction is being made in one structure and
not in the other then their coloumb energy values should be
different too, no? Wouldn't this be visible with simple energy
minimisation?
How different are they?
You mention you use encad with "full solvent". Does that mean you ahve
the protein
solvated in a box of water?
If your point is only to show that in one case you have an
electrostatic interaction and not
in the other you might just need to show that with an image! The
energies after minimization
are not necessarily more meaningful ...
I would prefer to not do molecular dynamics, because the structure
is biologically optimal in this conformation and molecular dynamics
may move it too much.
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