# Ligand docking: how to generate the crystal_complex.pdb with hydrogens added

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Ligand docking: how to generate the crystal_complex.pdb with hydrogens added
#1

Hello,

I'm having trouble with how to generate the crystal_complex.pdb with the ligand hydrogens added. I have tried cleaning the pdb while keeping the ligand with the clean_pdb_keep_ligand.py script but the ligand in reported crystal structure has no hydrogens. Using that crystal_complex.pdb for docking study gives error: " The native pose passed to InterfaceScorecalculator does not have chain X. " Is there a way we can clean the pdb, keep ligand, and add the hydrogens?

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Wed, 2020-06-17 15:03
nhinguyen26

If using the binaries and not pyrosetta, simply running the PDB though score, preferably with -no_optH false, will give you a structure with hydrogens.
Also this would be good to see if your ligand is still there —say you are running with -load_PDB_components false and -ignore_unrecognized_res true and no relevant topology files...

However, for docking you have to specify the the fold tree. It is rather user-focused (ie. no jumps and all that stuff like for loop modelling) and you specify what chains they are, say AB_C, it looks like that could be the problem —are the chains correct? Hydrogens are generally added happily —for a params file to work you need the first three atoms* listed in the internal coordinate block and the rest are added with a warning and hydrogens aren't one of them.

(* I think: HOH works though with O only and possibly any connect atom are a must? Anyway.)

Sat, 2020-06-20 03:56
matteoferla