Hi,
I have been trying to dock a protein and peptide at pH 5.5 using pH_mode as described by Kilambi and Gray's protocol. However, if I omit the keep_input_protonation_state flag the SFR builder removes the protons from the protonated residues. If I keep the keep_input_protonation_state flag I get a "can not find a residue type that matches the residue HIS_P" error. Is there a fix for that?
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Without keep_input_protonation_state flag
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 1 in file complex_0002.pdb. Best match rsd_type: HIS:NtermProteinFull
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 110 in file complex_0002.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 139 in file complex_0002.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 176 in file complex_0002.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 454 in file complex_0002.pdb. Best match rsd_type: GLU
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With keep_input_protonation_state flag
core.util.switchresiduetypeset: can not find a residue type that matches the residue HIS_P:NtermProteinFull at position 1
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Here is my input
-s complex_0002.pdb
-partners A_B
-dock_pert 3 8
-spin
-pH:pH_mode
-pH:value_pH 5.5
-pack_patch pH_pack
-high_patch pH_dock
-high_min_patch pH_min
#-keep_input_protonation_state
-ex1
-ex2aro
-unboundrot complex_0001.pdb
-nstruct 1000
Any help is much appreciated!
It looks like you're doing protein-protein docking. By default, protein-protein docking goes through a low-resolution "centroid" stage for the coarse-grain docking. The problem in this with pH mode is that there are no settings for the protonated residue types in the centroid representation.
There are several ways around this. First off, if you can get away with full atom refinement in your docking runs, you can avoid switching to centroid mode, and avoid the problem altogether.
Alternatively, you can do the low resolution and high resolution docking in separate runs, doing the low resolution docking with a regular HIS, and then switching to the pH mode protonated HIS for the high resolution mode.
A third way is to make "cheater" params files for the protonated forms. Go into Rosetta/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/ and you'll find the parameter files for the standard amino acids. Copy the appropriate ones (HIS.params in this case) to your running directory. Using a text editor, edit the copied params file to change the NAME line (and only the name line) such that it matches the non-patched name of the protonated form. (in your case, change `NAME HIS` to `NAME HIS_P`). Then when you run things, pass that modified params file to Rosetta by using the `-extra_res_cen` option. Although that won't treat protonated histidine specially in low resolution centroid mode, it should allow you to switch back and forth to centroid mode with pH mode enabled in the high resolution, fullatom refinement. -- Note that you may have to do the copy-and-modify with other residues (e.g. GLU) as well.