Modeling protonated histidine

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    • July 18, 2016 at 2:34 pm #2468
      Anonymous

        Hi,

        I’d like to model one of the histidines in my structure to be in a protonated form with hydrogens on the NE2 and ND1.  I see there’s a param file for protonated histidines (~/rosetta/database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states/HIS_P.params).  What’s the best way to specify in my pdbfile that I want that particular histidine to be protonated?

         I tried renaming the residue to “HIP” in my pdbfile and changing the first few lines of that param file to be:

        NAME HIS_P

        VARIANT PROTONATED

        IO_STRING HIP H

        TYPE POLYMER #residue type

        AA HIP

        ROTAMER_AA HIS

        But this doesn’t work.

         

        Thanks,

        Andrew

      • July 18, 2016 at 2:47 pm #11743
        Anonymous

          The one thing you’re missing is that reading in protonated variants isn’t enabled by default. Try adding the options “-keep_input_protonation_state” and “-pH_mode” to your commandline.  (It’s probably missing the latter, more than the former, that’s hurting you with your renamed file: if it’s not set, Rosetta ignores everything in the protonation_states directory.)

        • August 5, 2017 at 2:18 pm #13647
          Anonymous

            Yatta!

            I wanted to run a protonated histidine too. So I gave this a spin and got errors. One of the warning was that the HIP did not have a specified chirality, so I added the L_AA to the property line and inexplicably all worked. I did not change the geometry as suggested in another post. I have attached my HIP.params (remove the txt, which is there for upload reasons).

             

          • July 18, 2016 at 3:27 pm #11744
            Anonymous

              Thanks Rocco,

              I still can’t seem to get this to work.  I’ve tried using your suggestion (version 1 in my flags below) or specifying “extra_res_fa” and a protonated param file (version 2).  The only difference between this param file and the one in the rosetta database is that I changed “IO_STRING HIS H” to “IO_STRING HIP H”.  I renamed the histidine in my pdbfile to “HIP”.  Input pdb and modified params file are attached.  (NOTE: I also tried changing the HIS_P.params in the rosetta database to have the same “IO_STRING HIP H” line).

               

              Flags:

              -s input.pdb

              -relax:constrain_relax_to_start_coords

              -relax:coord_constrain_sidechains

              -relax:ramp_constraints false

              -ex1

              -ex2

              -use_input_sc

              -no_optH false

              #-flip_HNQ

              # === Version 1 === #

              -keep_input_protonation_state

              -pH_mode

              #-value_pH 6

              # === Version 2 === #

              #-extra_res_fa ./HIS_P.params

               

              Ran using:

              ~/rosetta/bin/relax.linuxgccrelease @prep_rosetta.flags

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