# patch file modification for ser_phosphorylated.txt

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patch file modification for ser_phosphorylated.txt
#1

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

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(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P](=O)(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])

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Post Situation:
Sun, 2020-06-21 00:49
hajar

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.

Tue, 2020-06-23 10:58
matteoferla