Ligand being read as part of protein structure

[Anonymous]

Hi,

I’m attemping a docking run with a protein that acts on an amino acid substrate. (tyrosine) Whenever I initiate the run it gives me the warning:

[ WARNING ] skipping pdb residue b/c it’s missing too many mainchain atoms:    1 W TYS TYR:CtermProteinFull:NtermProteinFull:sulfated

core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CA .

And then the error: 

[ ERROR ]: Caught exception:

File: src/core/pose/chains_util.cc:463

 chain_id W does not exist

I believe that it is not registered chain W, which is the designation of my ligand, because it is registering it as part of protein itself. However, that doesn’t account for why it believes a sulfur is involved in the process.

If I add the CA designation to my tyrosine ligand the run will go through but fill in the rest of the ligand (including erroneously adding a sulfur which is in no way part of any aspect of my run) but it will give a warning:

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  CB  on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD1 on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD2 on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  CE1 on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  CE2 on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  CZ  on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OH  on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  S   on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  O1  on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  O2  on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.conformation.Conformation: [ WARNING ] missing heavyatom:  O3  on residue TYR:CtermProteinFull:NtermProteinFull:sulfated 476

core.pack.pack_missing_sidechains: packing residue number 476 because of missing atom number 6 atom name  CB 

I have attached some relevant files, please let me know if there are any clarifications or further files I should upload. Thanks!

[Anonymous]

I think the issue you’re running into is that your custom params file is fighting with the regular TYR definitions. When Rosetta tried to load the PDB, it’s doing its best to figure out if that TYR residue is a standard TYR derivative, or if it’s your custom ligand. For whatever reason, it’s choosing to interpret things as a modified TYR, which leads to your issues.

My suggestion is to use a different three letter code for your custom ligand. Change your PDB input and the IO_STRING line to be something other than TYR. (e.g. YTR or TYY or TRL — basically, anything which isn’t a commonly used three letter code.). That should allow Rosetta to correctly match up the TRL (or whatever) lines in the PDB with the params file with the IO_STRING designation of TRL.

[Anonymous]

I’ve tried two different three letter codes (TRS and TYS) and oddly enough they give out different errors. For TRS, it gives the error: 

File: src/core/id/NamedAtomID_Map.hh:390

Residue outside res_map range

In the past I’ve only gotten this error when not having properly called a params file. 

When using the three letter code “TYS” is gives me the error “chain ID W not recognized” which is the same error I was receiving before where it wanted to read the tyrosine ligand as part of the backbone and sulfanate it for some reason. 

[Author]

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