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Protonation State

posted Nov 1, 2012, 9:52 AM by Dong Xu   [ updated Apr 11, 2013, 2:54 PM ]
Great article about basics:

http://www.daylight.com/meetings/emug00/Sayle/pkapredict.html

More pka examples:
https://docs.google.com/file/d/1LqtPkvhwlSDJpkxTV9ZCtz0-XgvHX_1HwNC8c3v9rjL-aFQ9xLJPokHON8py/edit?usp=sharing

1/ You know the pH you want for your simulation and you know the pKa of a certain residue, say His15, and now you want to know what to do about protons on the ND and NE. You have to decide on the following: If pH<pKa you protonate both nitrogens, otherwise you protonate one of them - which one could depend on possibilities of forming hydrogen bonds. 

2/ You want to know the pKa.
You can a/ look it up in a textbook, b/ look it up in a paper if somebody has measured it, c/ get somebody to measure it, d/ calculate it using Poisson-Boltzmann (there is a large literature on this subject)

Examples of Hendersen equation calculations are here:
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