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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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How to get the charge on each Amino residue? #164

Closed samit1194 closed 9 months ago

samit1194 commented 1 year ago

Hi,

Once pKa File is generated. It has the following columns to see the charges.

  1. Sidechain Hydrogen Bond: This column indicates the hydrogen bonding interactions involving the sidechain of the residue.

  2. Backbone Hydrogen Bond: This column indicates the hydrogen bonding interactions involving the backbone of the residue.

  3. 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?

YZXyinzhaoxu commented 9 months ago

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？