ab initio modeling using constraints

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    • #1826

        I am working on ab initio folding of a dimeric molecule using distance constraints.
        The constraints format being used is similar to NMR derived NOE constraints.
        But, data is not derived from NMR.
        I was wondering if that is the correct way to impose constraints on any general

        ~/rosetta. -seed_offset `echo $RANDOM` -cst ~/test.cst -cst_min -nstruct 10000
        -paths ~/paths.txt -output_pdb_gz -timer -fa_output -output_silent_gz
        -read_all_chains -randomize1 -symm_type cn -pose_fold_and_dock
        -docking_pose_symmetry -pose1 -slide_contact_frequency 0.01
        -rigid_body_frequency 0.01 -rigid_body_cycles 100 -new_centroid_packing
        -rg_reweight 0.0001 -move_anchor_points -monomer_input -pose_relax
        -pose_relax_fragment_moves -increase_cycles 1 -output_chi_silent
        -stringent_relax -ex1 -ex2 -vary_omega -omega_weight 0.5
        -docking_pose_symm_full -combinatorial_rms_sym
        -pose_symm_jump_moves_during_relax -pose_symm_n_monomers 2

        constraint format I am using:
        5 CEN 16 CEN 7.00 4.00
        5 CEN 81 CEN 7.00 4.00
        5 CEN 36 CEN 7.00 4.00
        36 CEN 63 CEN 7.00 4.00

        I am using rosetta v2.3.
        Are all these flags in order?
        Is there any other way of performing constraint based ab initio folding?

        Thanks in advance.

      • #9774

          The documentation for the Rosetta2.3 version of constraint files can be found at https://www.rosettacommons.org/guide/File+Format#_Constraints_Files You probably want the “Distance constraints (ab initio)” section. There’s an example at https://www.rosettacommons.org/guide/NOE+distance+constraints+examples as well.

          Things that jump out at me as important to keep in mind: There’s a several line header on the file. The format is column based as opposed to whitespace separated (so spacing matters). It looks like you’re missing the “Actual distance” field, although I’m not sure if that’s optional or not.

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