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GDP protonation state for QM

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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GDP protonation state for QM

Postby CoffeeIsTheColour » Mon Jun 21, 2010 10:10 am

Hi folks,

I planned to set up a QM system of GDP and Mg2+. The Mg2+ will be octahedrally coordinated with 4 H2O, the GDP BO- and a side chain OH residue. I would like some information on the best way in which to treat the GDP, in particular the protonation state of the B phosphate oxygen.

Any advice would be greatly appreciated.

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