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I want to perform a Molecular Docking between some ligands and a protein in different pH conditions.

For this, I calculated the distance between atoms in different pH concentrations for the ligands, using the software Avogadro.

I would like to do the same with my protein, that is, get the structure and its protonation state for two different pHs.

Is there any software that allows me to do that?

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H++

H++ is a web service that permits to protonate your macromolecules using using different pH conditions.

From its site:

H++ is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties.

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