On Mon, May 27, 2013, Bishnu Thapa wrote:
> I was trying to calculate free energy of deprotonation of protonated
> pyridine (pyridinium cation) in aqueous medium using explicit solvation
> model using AMBER. For this particular case, I manually made the VDW
> interaction of hydrogen being removed to zero and followed the AMBER
> tutorial A6. When I ran the thermodynamic integration calculations in
> gas phase and in aqueous phase, I came up with the free energy change
> more than 20 kcal/mol which in higher than the expected value. I know,
> the tutorial explained the relative pKa calculation (not the absolute).
This is hard to follow: you don't say what the "expected value" is, or even
exactly what you are computing. Nor do you say what results you got.
As you note, the tutorial (and MM calculations in general) only can provide
relative pKa's (for the same titrating group in different external
environments). You don't seem to be trying this sort of calculation.
It would be good for you to write down the thermodynamic cycle you are
evaluating.
...good luck...dac
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Received on Mon May 27 2013 - 19:00:02 PDT
