No Hydrogens in PDB files

[cryotheta]

The pdb files generated do not contain any hydrogen atoms, my simulations need complete structures with H atoms is there a way to add the H atoms?

[ausmeyer]

Most simulation frameworks have a tool for this as part of their pipeline.

If that won’t work, you can try a simple online tool like HAAD.

https://zhanggroup.org/HAAD/

PyMOL has a simple method to do it though I don’t know if it does any sort of optimization.