Dear Sir or Madam,
I have being tried to dock a ligand to the metal ion of an enzyme. Unfortunately, despite all efforts, the Rosetta (coupled_moves script) doesn't recognize the connection between negatively charged ligand's Nitrogen and Zinc (II) ion and assign two Hydrogens to that Nitrogen atom instead of desired one Hydrogen and the last spend valence for the Zinc ion. I have tried to write down both a direct bond (BOND_TYPE) withing PDB, MOL and .params files between these foregoing atoms as well as CONNECT between them.
Even more, I have written down the flags for metalloproteins.
Here there is a script which I execute:
~/rosetta_src_2020.08.61146_bundle/main/source/bin/coupled_moves.default.linuxgccrelease -s protein_with_ligand.pdb -resfile 4ww6.res -parser::protocol Dock_coupledmoves.xml -coupled_moves::backbone_mover backrub -coupled_moves::ligand_mode true -number_ligands 1 -ligand_weight 1.0 -in::auto_setup_metals true -in::metals_detection_LJ_multiplier 1.5 -in::metals_detection_LJ_multiplier 1.0 -in::metals_distance_constraint_multiplier 1.0 -extra_res_fa eza_nh.params -mc_kt 0.6 -boltzmann_kt 0.6 -packing::no_optH false -nstruct 2 -ntrials 500 -save_sequences true -save_structures true > Output_CM.txt
Would anyone here be kind to explain me how to write down the CONNECT records in params file in a proper way, which set up the connection between two desired atoms, please?
I attach both .params files (with BOND_TYPE and CONNECT records, respectively) to this post.
I will be highly appreciated for your response, and I am looking forward to your response.