Is there is a standard leap command to add hydrogen atoms to non-polar atoms (carbons) only during system building? I am preparing a protein-ligand system for MD from pdbqt protein-ligand complex and do not want to change the ligand tautomeric state. I tried rdkit, obabel, chimera but every tool I tried will add hydrogen to the entire molecule, not carbon atoms only? Any suggestion?
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Received on Tue Apr 28 2020 - 14:30:02 PDT
