Problems with Cterm_amidation.txt

[Anonymous]

Hi everyone,

 

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  

-in:Ctermini C

 

[Anonymous]

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.

 

[Anonymous]

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.

[Anonymous]

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. 

[Anonymous]

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. 

[Anonymous]

And how do I specify that the path should only be applied to chain C? Thanks!

[Anonymous]

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:

• the OXT atom to N space space —to keep the column order which is important in a PBD fiel.
• The element from O –> N
• The residue number +1
• The residue name is NHH

   

 

 

 

[Anonymous]

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.

 

[Anonymous]

Thanks!

[Author]

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