I'm looking foward to use the SnugDock protocol. I did read both "SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models" (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000644) and "Modeling and docking of antibody structures with Rosetta" (https://www.nature.com/articles/nprot.2016.180) articles.
Also, I read the SnugDock web page in https://www.rosettacommons.org/docs/latest/application_documentation/antibody/snugdock .
The problem is that the description of the protocol in the website is different from the articles. In the webpage are mentioned a lot of flags that theoretically should be used in the protocol that are not mentioned in the articles.
For instance: In the articles, after modeling all the structures for the ensembles and prepacking them, the authors only says to run the command snugdock.mpi.linuxgccrelease -s antibody_antigen_start.prepack.pdb -ensemble1 antibody_ensemble.list -ensemble2 antigen_ensemble.list -antibody:auto_generate_kink_constraint -antibody:all_atom_mode_kink_constraint -nstruct 1000
but in the webpage manual it says that all the following flags should be used: snugdock.mpi.linuxgccrelease -s input.pdb -native native_input.pdb -out:file:scorefile score_out_snugdock.sc -out:path:pdb models_path_out -out:pdb_gz -nstruct 1000 -constraints:cst_file kink.cst -constraints:cst_weight 1.0 -constraints:cst_fa_file kink.cst -constraints:cst_fa_weight 1.0 -partners LH_G –spin -dock_pert 3 8 -h3_filter false -kic_rama2b -loops:ramp_fa_rep -loops:ramp_rama -kic_omega_sampling -allow_omega_move true -loops:refine_outer_cycles 3 -loops:max_inner_cycles 80 -ex1 -ex2aro -talaris2014 true
I'm aware that some of these additional flags should be used only if I need/want (like constraints flags, output flags) but there are several others flags that seem to be important. So, should I only use the flags described in the articles or use all the options mentioned in the protocol webpage?
Thanks in advance,