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clauswilke / PeptideBuilder

A simple Python library to generate model peptides
MIT License
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No Hydrogens in PDB files #48

Open cryotheta opened 2 years ago

cryotheta commented 2 years ago

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 commented 2 years ago

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.