I'm a new user of Rosetta. The CryoEM protocol provided by Dimaiolab is excellent.
My protein contains a peptidyl carrier protein domain. The peptidyl carrier protein domain has a prosthetic group Phosphopantetheine which is conjugated at a serine residue. More complicated is that the phosphopantetheine arm carries a cysteine peptide group via the terminal thioester linkage. I don't know how to model this peptidyl carrying phosphopantetheine arm into the CryoEM map and then perform the iterative or simple refinement against the map.
Whether I should draw a peptidyl-phosphopantetheine structure first? And then convert it to a pdb file? Can I draw the chemical using pymol, so that it can be saved directly? I know I should then again convert it to mol2 file using OpenBabel. After that molfile_to_params.py can be employed to obtain two params files.
Since the phosphopantetheine is conjugated to the serine residue, how should I tell rosetta that it is convalently bound?
Should I also need to link the peptidyl-phosphopantetheine to the serine residue in the peptidyl carrier protein domain model first using Coot before the Rosetta simple relax refinement against the CryoEM map?
And are there other materials I should prepare?
Thanks so much for your help.