Is there a way to convert a pdf file that cotains only a ligand from one protonation state to another?

14 November 2022 0 7K Report

I have been looking for a way to create pdb files with a ligand in different protonation states. I came across this Article Dimorphite-DL: An open-source program for enumerating the io...

article and tried the python package described but the outcome is in smiles form and I am not really sure it works. I also tried Avogadro and obabel GUIs but the option add hydrogens for this ph works on residues only. Is there something I am missing?

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