How to get the charge on each Amino residue?

[samit1194]

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]

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？

[sobolevnrm]

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？

This question is answered in #174 .

[sobolevnrm]

Which columns must I consider for calculating the charge on the Amino residue? and what is the logic behind it?

It is probably easier to extract this information from a PQR file generated by PDB2PQR. PDB2PQR uses PROPKA as its backend for predicting the pKa and titration state but then assigns charges based on that information.