Hi,
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).
Is it possible to run the explicit solvation calculation for such system I mentioned above? If yes, what should be my input files and what factors are necessary to consider?
I have attached some of the input files that I had used for calculation. I will appreciate your help and suggestions. Thank you so much.
Sincerely,
Bishnu Thapa
Chemistry Department
Wayne State University
Detroit, MI
USA
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Received on Mon May 27 2013 - 15:00:02 PDT
