Reply To: Using Patches in Rosetta

[Anonymous]

Generally speaking the patched residue types are automatically detected by the PDB reader. So, if you’ve already got a PDB, it ought to apply automatically for any structure that has one. This would work for most applications that take PDBs.

Abinitio is not my area of expertise, but I believe there’s an “extended FASTA” format brewed up for Rosetta. Here’s an example from one of the metalloprotein abrelax benchmarks:

PPGLC[CYZ]PRC[CYZ]KKGYH[HIS_D]WKSEC[CYZ]KSKFDKDGNPLPPZ[ZN]

I think if you put your SO3-Tyr in with the [syntax] it might work. I think the patched name is [TYR_p:sulfated]. If this is a terminus residue, or has anything else weird about it, that name needs to change to reflect it.

Also, make sure the patch is on by default in patches.txt (which I assume you found…)