I am trying to use Cterm_amidation.txt. I would like to replace -OH in the C-terminal end with -NH2. However, I get the following error
[ WARNING ] discarding 1 atoms at position 9 in file MUT_374ILE_375LEU_376GLY_377THR_378VAL_379SER_380TRP_381ASN_382LEU_bj1_C.pdb. Best match rsd_type: LEU
core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 9 with connection point 2
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 9 atom OXT (trying to store temperature in PDBInfo)
It deletes O (OXT) but does not add -NH2.
My files look like this:
ATOM 6080 N LEU C 9 44.877 19.664 18.478 1.00 0.00 N
ATOM 6081 CA LEU C 9 45.506 20.023 19.738 1.00 0.00 C
ATOM 6082 C LEU C 9 45.047 21.355 20.331 1.00 0.00 C
ATOM 6083 O LEU C 9 45.571 21.728 21.398 1.00 0.00 O
ATOM 6084 OXT LEU C 9 44.580 22.203 19.563 1.00 0.00 O
ATOM 6085 CB LEU C 9 46.988 20.118 19.534 1.00 0.00 C
ATOM 6086 CG LEU C 9 47.663 18.923 18.940 1.00 0.00 C
ATOM 6087 CD1 LEU C 9 49.003 19.313 18.804 1.00 0.00 C
ATOM 6088 CD2 LEU C 9 47.499 17.643 19.766 1.00 0.00 C
ATOM 6089 H LEU C 9 45.317 19.864 17.568 1.00 0.00 H
ATOM 6090 HA LEU C 9 45.279 19.240 20.451 1.00 0.00 H
ATOM 6091 1HB LEU C 9 47.177 20.968 18.875 1.00 0.00 H
ATOM 6092 2HB LEU C 9 47.459 20.320 20.491 1.00 0.00 H
ATOM 6093 HG LEU C 9 47.268 18.730 17.959 1.00 0.00 H
ATOM 6094 1HD1 LEU C 9 49.534 18.560 18.363 1.00 0.00 H
ATOM 6095 2HD1 LEU C 9 49.037 20.198 18.181 1.00 0.00 H
ATOM 6096 3HD1 LEU C 9 49.400 19.526 19.778 1.00 0.00 H
ATOM 6097 1HD2 LEU C 9 48.030 16.829 19.280 1.00 0.00 H
ATOM 6098 2HD2 LEU C 9 47.881 17.777 20.739 1.00 0.00 H
ATOM 6099 3HD2 LEU C 9 46.460 17.394 19.823 1.00 0.00 H
-ex1 -ex2 -flip_HNQ -no_optH false -use_input_sc -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -relax:cartesian -beta -score:weights beta_nov16_cart.wts -ignore_zero_occupancy -missing_density_to_jump -nstruct 3 \
-extra_patch_fa /path/to/file/Cterm_amidation.txt \
-s MUT_374ILE_375LEU_376GLY_377THR_378VAL_379SER_380TRP_381ASN_382LEU_bj1_C.pdb \
Curious. It does not work in pyrosetta either (`pose_from_sequence('AAA[ALA:Cterm_amidation]')`). Looking at the patch there is a note at the bottom saying that stuff is in the wrong place. Copying the code between delete atom (not inclusive) and the first END_CASE (not inclusive) and pasting between the very final BEGIN_CASE END_CASE lines makes it work.
I've not tried with the binary, but if it does not work, delete the OXT from the input or change it to name ` NT ` and element N.
In case someone else was wondering, there is not a terminal residue for an primary amide. There is an N-methylamide (NME), which works like the N-terminus cap ACE, ie. its in the standard residue type set. PyMol builder adds a residue called NHH which is not the correct PDB name for it —NH3 and NH4 are the free ligands.
Actually, if you (OP) want an amide to make it more like a part of a longer peptide N-methylamide is a better call, not to mention it is a normal cap from a peptide from a synthesiser.
This will be fixed shortly in master (though the quick-and-dirty solution is to remove the NOT VARIANT_TYPE UPPER_TERMINUS_VARIANT line from the Cterm_amidation.txt file in Rosetta/main/source/database/chemical/residue_type_sets/fa_standard/patches). Note, though, that the relax app isn't trying to add this patch -- the relax app doesn't do custom patching. To add the patch and relax, please use the ModifyVariantType mover and the FastRelax mover in that order in RosettaScripts. Also note that the -extra_patch flag is not needed; the Cterm_amidation patch is loaded by default.
Thanks both. matteoferla, it did not work. I tried to it manually, replacing OXT with NT and O with N. However the relaxation could not recognize NT, decarding the atom.
How is the path itself supposed to be used? replacing OXT with NT in a way NT can be recognized in the following relax step.
And how do I specify that the path should only be applied to chain C? Thanks!
As mentioned, I had just tried the patch in Pyrosetta —I had assumed that there may have been some flag I was unaware for the Rosetta Relax binary that added patches on demand. But as Vikram said, this is not the case.
Given this and that you want to mutate a specific chain, you'll have to use scripts if you want to apply a patch. https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/MutateResidueMover with new residue with the 3-letter code colon and patch name, is one way...
..Alternatively, you can do something a bit nasty: use a terminal residue for the nitrogen cap —I assume using N-methylamide (NME) was not good for your plans. I made one and tried it (attached).
I called the terminal residue cap `NHH` like PyMOL calls it. This is a taken PDB residue name so if something misbehaves use `-load_PDB_components false` flag. So edit the PDB by changing:
I just realised I made a mistake yesterday, a C-terminal cap is `*[NH2]` not `*[NH3+]` as it is bound to the C-terminus, it's an amide.