Reply To: flexpep docking problem—–How to do with phosphorylation peptide?

[Anonymous]

Presumably you want to model the phosphorylated residue. I’m going to assume it’s phosphoserine, but this advice works for any of them.

First, make sure p-ser is active in the residue type set. Go to minirosetta_database/chemical/residue_type_sets/fa_standard/patches.txt and make sure the proper phosphorylated residue type is active (NOT commented out with #). (This is default).

Next, make sure Rosetta reads it in. Make sure your atom names in your input PDB match the atom names specified in the patch file (its path is in patches.txt). Spacing will matter here, ” P ” is different from ” P “.

Run short trajectories as you test the PDB read in, or just run something like the score app, and look at the output to make sure Rosetta keeps the phosphoatoms in place.

Once the PDB reader handles it, flexpepdock should as well.