force hydrogen rebuild on input

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    • #1760

        Hi all,

        Was just wondering, are there any options I can use to force Rosetta to ignore PDB defined hydrogens and rebuild all hydrogens (including non-polar) when loading into the score, relax, rosetta_scripts Apps? I particularly need to rebuild backbone non-polar hydrogens as these are bad in the input PDB files but Rosetta generally seems to leave these untouched.

        I have tried the options:

        -no_optH false
        -skip_hydrogens true

        but these didn’t appear to have the desired effect. I could, of course, delete these in the input file but was wondering if there was a way of doing this with some flag.

        thanks for your help!


      • #9508

          I’m not aware of any such option, and looking at the code, I don’t think there is one. Physically deleting them from the input file is the recommended course of action. (It should be relatively quick to remove all the hydrogens with the appropriate grep command. “egrep -v ‘.{13}H’ withH.pdb > withoutH.pdb” should do it for you in most cases, assuming typically named hydrogens.)

          -no_optH false will rebuild hydrogens, but only for those hydrogens which may be misplaced or poorly specified on sidechain residues. (e.g. histidine protonation states, or hydroxyl rotamers). It doesn’t touch hydrogens which don’t typical have degeneracy (e.g. nonpolar hydrogens), and it doesn’t touch backbone hydrogens.

          -skip_hydrogens is specifically for the SAXS score function (the full name is -scoring:saxs:skip_hydrogens), and is ignored even there.

        • #9510

            thanks for the answer.

            I just deleted the backbone hydrogens in the end.

            I noticed you can get weird energies if you are not careful because it looks like fa_atr is turned on for hydrogens but fa_rep is turned off.

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