patch file modification for ser_phosphorylated.txt

[Anonymous]

Hello,

I have a modified residue named SPF in my pdb which is composed of Serine + Phosphopanthenine arm +acyl with SMILES  below.

I noticed phosphorylated SER exist in Rosetta database. Therefore,  I decided to model this modified residue by modifying ser_phosphorylated.txt patch file. My new patch and pdb file file has been attached.

After relaxing the pdb file with the option -extra_patch_fa ser_phosphorylated_acyl.txt in the following way:

relax.static.macosclangrelease -linmem_ig 100 -use_input_sc -nstruct 1 -relax:fast -relax:constrain_relax_to_start_coords -scorefile relax.fasc -s C14.pdb -out:prefix relax -extra_patch_fa ser_phosphorylated_acyl.txt

I get an error saying

core.chemical.Patch: [ WARNING ] Patch phosphorylated implies it can apply to residue type SER, but actually applying it fails.

core.chemical.Patch: [ WARNING ]    You may want to check your patch definitions.

core.chemical.Patch: [ WARNING ] Patch phosphorylated implies it can apply to residue type DSER, but actually applying it fails.

core.chemical.Patch: [ WARNING ]    You may want to check your patch definitions.

ERROR: Unrecognized residue: SPF

ERROR:: Exit from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 1403

 

I am not sure what is wrong with the patch file. I did  not change NAME (phosphorylated) and TYPES (PHOSPHORYLATION) in the biggening of the patch file. Do I need to change them?

What I did is:

1. Replace SEP with SPF

2. Add new extra atoms

3.add new bonds

4. add Internal coordinates

 

by the way, I did not add any chi angle. Does patch work without the new chi angles? If not, how can I get the chi angles for my modified residue?

 

I would be grateful if you could help me.

 

 

hajar

 

 

 

 

(CCCCCC()SCCNC()CCNC()[C@@H](C(C)(C)CO[P]()(O)O)O.N([C@H](C=O)C(O[P](O)(OC(C(C([H])([H])[H])(C([H])([H])[H])[C@@H](O[H])C(N(C(C(C(N(C(C(SC(O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])O)([H])[H])([H])[H])[H])O)([H])[H])O)([H])[H])[H].N([C@H](C=O)C(O[P](O)(OC(C(C([H])([H])[H])(C([H])([H])[H])[C@@H](O[H])C(N(C(C(C(N(C(C(SC(O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])O)([H])[H])([H])[H])[H])O)([H])[H])O)([H])[H])[H])

[Anonymous]

Why not simply make a non-canonical amino acid?

• You appear to have parameterised the compound anyway…
• Patches are tempramental
• Textediting topology files aways causes issues (as here)

   

The Chi is not at all the problem –omitting them does not crash Rosetta (it removes degrees of freedom in internal coordinate mode).

In your PDB your serine is distant: when you import the pose that jump will be not be closed. Remodel can close it (synthax is odd for NCAA), alternatively, if you have a version without the SFP residue, simply rename the correctly placed residue in pymol `alter resi 36, resn=’SFP’` or in text editor and the missing atoms are replaced —try it with SEP or with a NCAA code.

I gave it a gander and it looks okay, so it must be typo somewhere. In case someone else wants to check. These are some notes of simple checks that are correct

• The residue in the PDB provided is ATOM, not HETATM
• The SMILES contains multiple molecules (`.`), but the parts aren’t repeated, only the first
• The PDB file atom name seem to match
• Changing the name to something unique (e.g. acetylphosphated), does not stop it from crashing —tested in pyrosetta using ‘1UBQ’ (in case it was the PDB) and pyrosetta.rosetta.protocols.simple_moves.MutateResidue(target=20, new_res=’SER:acetylphosphated’).apply(pose), while :phosphate patch works fine.

 

 

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