I have a pdb with the hydrogens already in it. I would like to keep the some specific hydrogens (on the amide nitrogen of a n terminal residue) in the same orientation as the crystal structure. The -no_optH flag doesn't seem to do anything (same output weather set as true or false).
I am aware of the possibility to work in constraints, but this is less desirable than keeping the native structure as it is.
This is what I'm running: FlexPepDocking.macosgccrelease -database ~/software/rosetta/rosetta_database/ -s input.pdb -receptor_chain 'A' -peptide_chain 'C' -native input.pdb -out:prefix score_ -flexpep_score_only -no_optH true -use_input_sc >> score.log
Another developer, Matt, has spent a lot of time fiddling with hydrogen bonds (sensitive to hydrogen placements). He says:
"My impression is that if the hydrogens are there, it keeps them, if they aren't, they are placed and then optimized their position if the the -no_OptH flag is false.
To test this, they can remove the hydrogens (delete the HATOM rows in the pdb) and see that they are placed differently (e.g. by measuring their geometry in pymol)."
I would add a further note: Do you see lines of output mentioning that the PDB reader is rejecting atoms from residues? Hydrogen nomenclature is not very standard, so Rosetta often jettisons NMR hydrogens because they aren't named to the PDB standard that Rosetta uses. I forget the exact statement but it's something like "rejecting N atoms from residue 123: best match: ARG". You'd see a whole lot of them in a row.
yes,that's exactly what happened. The pdb used H1 and rosetta uses 1H etc (note you have to shift the column in the pdb so that the 1 in 1H overhangs onto the previous space). I just renamed the important hydrogens by hand. I bet someone has written a script to convert the names...