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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