Build polar H atoms and assign partial charges in PDB file

Useful for electrostatic calculations such as Poisson-Boltzmann solvers etc...

Partial charges are assigned according to Charmm22 parameters...

They are written in the B-factor column of the output PDB file, while the Occup. column is assigned to atomic radius.

N.B. This output format is essentially the PQR format, which is needed as input for AquaSol!


FAQS: a common mistake involves PDB files that contain OT1 and OT2 atoms for the terminal carboxyl group; the program needs O and OT, namely The carboxyl oxygen "O" is compulsory.

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PDB file to be checked


Report Potential energy : (1) VdW only; (2) Electrostatic only; (3) Both



Input data formats