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Hi, looking for some help,
It appears that constraints do not contribute to the final score output when running the FlexPepDock ab initio protocol.
I am getting docking samples that should yield score penalties >1000 under the provided distance constraints (AtomPair FLAT_HARMONIC). However, the scorefile reports numbers consistent with the score absent of penalties (approx -550, for a protein length 300 and peptide length 5).
I provide the constraints file with the flag -constraints:cst_file
I am trying to model a loop with a constraints file (the constraints are for the atoms of the loop).
but every time I get this message:
[FILE]: src/core/pose/util.cc [LINE]: 704 [START_MESSAGE] Atom 'OVL1 31' not found [END_MESSAGE] [END_CRASH_REPORT]
I also tried to set the flag "-constraints:named" to true but it didn't help...
I am using the following command:
I am setting up Docking simulations of 2 Monomers of a protein that forms monolayers at interfaces (HFBI, pdb entry 2fz6 ), so I need to constrain the possible Docking configurations to stay within the x-y plane and only beeing allowed to slightly change its orientation, due to a exposed hydrophobic patch.
I tried to use a combination of 2 angular and one Dihedral constraints. The constraint file looks like:
I am performing Rosetta ligand docking for an enzyme A to a ligand X which should be covalently bound to a small protein B. I need to impose this covalent bond and some other catalytic constraints (distances between ligand and receptor's residues and also the distances between two residues of the receptors ) to my ligand docking. I found several movers for adding constraints including AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover, but I am confused about which one works with Rosetta Ligand docking.
I am performing Rosetta protein-ligand docking and I added constraints both in centroid mode and high resolution mode, but the constraints are not used. I got a warning at the end of the log file saying :
protocols.jd2.JobDistributor: [ WARNING ] The following options have been set, but have not yet been used: