Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › neutral N-term and C-term
- This topic has 7 replies, 4 voices, and was last updated 3 years, 11 months ago by
Anonymous.
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June 9, 2013 at 5:20 pm #1607
Anonymous
hi all,
I want to create a peptide with N-term N atom unprotonated and C-term C atom protonated.
like NH2-ALA-GLY-PRO-COOH
How to do that?Thanks.
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June 10, 2013 at 6:15 pm #8884
Anonymous
You’ll need to patch the N-terminal and C-Terminal residues. Unfortunately, it doesn’t look like there’s an existing patch to do this in the way you want. Take a look at rosetta_database/chemical/residue_type_sets/fa_standard/patches/ directory for examples. The AcetylatedProteinNterm.txt and MethylatedProteinCterm.txt files are likely good starts.
Once you have created your patch files, you can load them into Rosetta (3.5) with the -extra_patch_fa command line flag. Then if your input PDB has the atoms from the patch present (you have to be careful to match the names exactly), the patch should be applied to the residue type for that residue. (If the output PDB contains the atom, then you know your patch worked.)
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February 28, 2014 at 11:33 pm #9847
Anonymous
Hi,
I am trying to handle my peptide which has amidated Cterm. I am using the patch at Rosetta/main/database/chemical/residue_type_sets/fa_standard/patches/Cterm_amidation.txt. However the relax apps didn’t recognize the NH2 residue type. Any idea why?
Thanks a lot, -
March 1, 2014 at 11:43 am #9848
Anonymous
Hi tigerous,
please take a look at the rosetta_database/chemical/residue_type_sets/fa_standard/patches.txt file. Check to make sure that the lines for the patch file you’re using are not commented out. (That is, they don’t have a “#” character before them.)if that’s ok then check that atoms are named correctly ( look at the patch file for atom names )and the alignment of the atom names is correct.
best,
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March 3, 2014 at 6:14 am #9849
Anonymous
Hi nawsad,
It was not commented out. What do you mean about correct atom names? I attached the peptide and the patch file below. I hope you can help.
Thanks, -
March 31, 2014 at 9:55 pm #9934
Anonymous
It works perfectly!
Thanks Rocco. -
October 8, 2020 at 12:29 pm #15539
Anonymous
Hi all,
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 -out:suffix _bn16_calibrate -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
-in:Ctermini C
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March 18, 2014 at 5:06 pm #9903
Anonymous
Rosetta handles N and C terminal modifications as an alteration of the main residue type, rather than as a residue type in and of itself. That’s what the patch files are doing. They’re not making a completely separate residue type, they’re instead “patching” an existing residue type. So you don’t get just a “c-amidation” residue, instead you get “alanine with c-amidation”, “lysine with c-amidation”, “histidine with c-amidation” etc.
So in your input PDB, you need to take the NH2 residue and make it be part of the preceding residue ( ALA 22 in this case). Additionally, you need to make sure the atom names on the amidation match up with those used in the patch file. (So the N of the amidation should be renamed to NT, and the HN1 and HN2 should be renamed to 1HE2 and 2HE2.)
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