Could anyone tell me how to model the structural change of one specific residue with phosphorylation? Thank you very much.
Your question is fairly vague. Do you have a phosphoX in your input PDB already? Do you want to mutate something into a phosphoX?
Sorry for that. I have already got the PDB without phosphorylation. And I know which residue have been phosphorylated. How to model the structure with phosphorylation? Thanks.
I've never tried it before, but the fastest thing to do is probably this:
A) look for the phosphoserine patch rosetta_database/chemical/residue_type_sets/fa_standard/patches/ser_phosphorylated.txt. It identifies the extra atoms you need.
ADD_ATOM P Phos X 1.50 ## Best guess from the small molecule ligand params file generator molfile_to_params.py
ADD_ATOM O1P OOC OC -0.78 ## The charge is taken from the free oxygen atoms of the phosphate backbone in DNA residues
ADD_ATOM O2P OOC OC -0.78
ADD_ATOM O3P OOC OC -0.78
B) Add these atoms (" P ", " O1P" etc) to the residue you care about in the PDB file. Be careful with the atom's name spacing. Leave the coordinates at 0/0/0.
C) Try repacking the residue to properly using fixbb and a resfile. Even score.cc might repack it for you; I know Rosetta automatically repacks residues with missing/zero occupancy atoms, but we don't want it to throw out the PO4 atoms; you can try leaving their occupancies at 0 (or deleting one of the O) and seeing it it rebuilds it automatically.
D) hopefully this will result in a structure with the P04 in place. From there, Rosetta protocols that do NOT use centroid phases should be compatible; if there are centroid phases then you'll have other problems (refer to this other thread: http://www.rosettacommons.org/node/2342)
Thank you very much for your reply. I'll try it out right away. However, I am wondering if I should relax the structures in the beginning and end of the process.
If it's on the surface it's not going to make much of a difference. If it's not on the surface, then probably yes.
Thanks a lot.
When I use the following resfile:
132 A NC K EX 1 EX 2
I got only one conformation of the sidechain of the modified lysine when generating multiple structures (the same rotamer as the unmodified one). How could I load the rotamer library of modified residues?
Maybe Rosetta thinks it's the best rotamer. Does it says "generating X rotamers at Y positions" or something similar?
I believe if it's a phospholysine, you should be able to convince Rosetta to use the existing lysine rotamer library instead of having to create your own. If you WANT to create your own, I'll put you in contact with someone who's good at it.
Did you create a phospholysine residue type, or did you modify one of the phosphorylation patches to apply to lysine?