patch file modification for ser_phosphorylated.txt

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.

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])