On Tue, Apr 25, 2023, Rory Crean via AMBER wrote:
>
>I've therefore been working on trying to place harmonic restraints to
>prevent the sodium ions from coming too close to the phosphate groups.
First, I agree with Christina here: is this what you really want to do? How
will you avoid overemphasizing phosphate-repulsions? And, how could you
justify any quantitative results you find with such ad hoc modeling?
Second, the "NMR" distance restraints are not set up for periodicity. The
distance between a given sodium and a given phosphate may not represent the
closest distance between that Na and all of the image phosphates in other
unit cells, especially given the high mobility of ions.
So, I don't immediately see any way in Amber to achieve your goal. Maybe
others on the list have ideas.
....dac
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Received on Tue Apr 25 2023 - 14:00:02 PDT
