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A PQR file of a protein describes the positions in $x$, $y$ and $z$ and the charges of every atom in it. If you have them, you can construct the charge density $\rho(x)$ of the protein, then use it to find the potential $\phi(x)$. The Boltzmann distribution is useful when you can't or don't know how to build the $\rho(x)$.

So is it necessary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file?

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So Is it neccesary to use Poisson - Boltzmann equation if I only need to build electrostatic potential from a PQR file?

No. You can use Poisson.

Since you know the positions of each point charge, you know the charge distribution $\rho$, which is a sum of delta functions.

You can thus solve numerically the Poisson's equation that links the charge distribution to the laplacian of the potential:

$ \begin{equation} \Delta V=\rho \end{equation}$

The solution will depend upon your boundary conditions. Also, many algorithms are available to find this solution.

One example may be found here on the arXiv. This paper is called "Efficient solution of Poisson's equation with free boundary conditions".

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