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Excuse me, I was wondering where “python-m propka” will be used after downloading the propka python module? Use it in python/ jupyter notebook, or in windows power shell?
Hi,
Once pKa File is generated. It has the following columns to see the charges.
Sidechain Hydrogen Bond: This column indicates the hydrogen bonding interactions involving the sidechain of the residue.
Backbone Hydrogen Bond: This column indicates the hydrogen bonding interactions involving the backbone of the residue.
Coulombic Interaction: This column provides information about the coulombic interactions of the residue.
To assess the protonation states, I can compare the pKa value with the pH of the solvent, along with the respective charge on the Amino residue.
Since I will be using the AMBER FF, ASP would need to be renamed as ASH, and likewise for other Amino acids.
Which columns must I consider for calculating the charge on the Amino residue? and what is the logic behind it?
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