Dear community,
I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.
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
Hi,
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:
Hello,
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:
AngConstraint.cst:
"
Hello,
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.
Hi, everyone!
Hello,
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:
-constraints:cst_fa_file ../input_files/myconstraint.cst
-constraints:cst_file ../input_files/centroid.cst
-constraints:cst_weight 10
Hello,
I am performing protein-protein docking with multiple constraints. I applied the constraints in full atom mode with these two commands:
-constraints:cst_fa_file myconstraint.cst
-constraints:cst_fa_weight 10
Generating Constraints File and Pre-Minimization Problems with ddG_Monomer Application -
Hello,
