I want to ask a question.
I have some protein structure and i want to calculate their score and chose the one which has lowest score. I used “score_jd2.mpi.linuxgccrelease” to get score.
But the output file pdb has different Hydrogen coordinate even I used the command “no_optH true” to keep the Hydrogen atom position.
I dont understand why it happened.
and which structure should I use for following job? the inital structure of the output pdb after running score command?
Thank you so much.
My guess is that you’re running into a hydrogen atom naming convention issue. Rosetta uses the older hydrogen atom naming convention for PDBs. PDBs from other sources don’t necessarily.
The result of this is that Rosetta will ignore “misnamed” hydrogens, discarding their coordinates. It will then rebuild the “missing” hydrogens according to ideal geometry. This will happen regardless of Rosetta application, so it doesn’t really matter if you use the original pdb or the scored output pdb – Rosetta will transform them both to the same thing internally, anyway.
If the exact positions of the hydrogens matter to you, I’d recommend renaming them in your input PDB to match Rosetta conventions. (Most of the time the exact hydrogen positions don’t matter, and would probably need to be refined to fit into the Rosetta energy function, anyway.)