I am super new to HADDOCKING!!! through tutorial I understood on how to perform docking involving two proteins but I have a specific case where I couldn’t understood everything. So I posting my question to get few feedbacks.
I have to dock a protein + peptide(where one of the Cysteine residue is MTSL spin labelled).
I have a pdb for a receptor, for peptide I dont have pdb, so I created using coordinates using XPLOR(where there is an option to for CYSP(Cys with MTSL spin label)).
My question are,
DO I have to prepare the pdb (peptide+MTSL) in HADDOCK format, i.e nomenclature of HADDOCK “CYM” residue is same as “CYSP” residue of XPLOR/CNS. I didnt find a “CYM” pdb to compare with CYSP pdb.
Which interface would be suitable to run receptor+peptide-MTSL docking, I am asking because initially I am going to use only CSP data from NMR followed by I want to use distance restraints from PRE data. Again I can only input AIR for receptor and for peptide we have any restraints. In this scenario should I leave the restraints option black?
In another case, I have to dock a protein with a ligand(organic) I have again created a topology and parameter file for this ligand using http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg, again the topology and parameter for ligand is in CNS format. Therefore for protein+ligand docking do I have to use guru interface? Is there is a option to upload my topology and parameter file in to HADDOCK.
I would highly appreciate your comments, suggestions,
Have good weekend…
With many thank…