neutral N-term and C-term

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.)

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,

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,

It works perfectly!
Thanks Rocco.

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

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.)