[chimerax-users] protonation of small molecule

[Enrico Martinez]

Dear ChimeraX users!
I need to protonate a small molecule from the input pdb file producing
another pdb with the protonated ligand.

I use the following batch script:

open 'ligand_without_H.pdb'
addh hbond false
save ligand_with_H.pdb displayedOnly true
exit

Depending on the complexity of the input 3D structure of the ligand
some protons could not be added so the final protonation state is not
correct. Is there a possible way to fix this issue?
Many thanks in advance
Enrico