I need to do certain symmetric docking to generate its homodimer and homotrimer and I am using Rosetta 3.4 Symmetric docking to achieve it.
I used the following command to generate homodimers :
./bin/SymDock.linuxgccrelease -docking:dock_ppk -symmetry:symmetry_definition ./sym_def_dimer.dat -symmetry:initialize_rigid_
body_dofs -database ../rosetta_database/ -out:nstruct 2 -out:file:fullatom -s S_00000001.pdb
I used to use the older version of Rosetta i.e Rosetta++2.1.2 where I used the following comman to generate homotrimers but now I use rosetta 3.4 and can't find its equivalent.
./rosetta.gcc64 a1 t000 _ -dock -symmetry -n_monomers 3 -nstruct 500 -s
n_monomers 3 : This enables us to generate homotrimers but the new Rosetta 3.4 does not have this option.
I will be grateful if you could help me with the proper command that would help me generate homotrimers from single monomeric unit(i.e PDB files) in rosetta 3.4 especially more so because I want to avoid using "fold and dock" instead.
Hopefully someone else with more knowledge of symmetric docking will be along to help, but from the limited amount I know about symmetry in Rosetta3, the type of symmetry is specified in the symmetry definition file. (See http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d1/d... along with http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/db/d... and http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d4/d... - take another look at http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d4/d... while you're at it, too).
If you wish to do trimeric docking, you need to create and specify a symmetry definition file which defines the trimeric symmetry you want to use, which substitutes for (and is more general than) specifying the number of monomers.