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Using a molecular viewer like PyMOL, I understand that its often incorrect to simply look at positive and negative residues and use those residues to calculate the charge density and instead, you should be using something like APBS to calculate the electrostatic potential.

What is the correct way of going about this?

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One way to do it is to perform a quantum chemistry calculation of the electrostatic field generated by the molecule. Another is to determine (or assume) partial atomic charges for each of the atoms of the system, and use a Poisson solver (as I believe APBS is) to calculate the electrostatic field generated by this point charge distribution.

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