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Constraints

Issues with angle Constraints during Docking

Category: 
Constraints

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:
"

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constraints in Rosetta ligand docking (AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover)

Category: 
Constraints

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. 

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constraint are not imposed during protein-ligand docking

Category: 
Constraints

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

 

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reading of AtomPair failed in relax with constraint

Category: 
Constraints

Hello,

I am relaxing a protein with a chemically bound ligand (attach as C14_SPF). The ligand is composed of Phosphopantethine and acyl together which are bound to ALA (residue 36 of chain B) of my protein. Actually, the residue 36 was originally SER which is bound to Phosphopantethine and acyl, but for modeling I took the OG of SERin Phosphopantethine and converted SER to ALA.

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How to specify constraints during fold-and-dock?

Category: 
Structure prediction
Docking
Constraints
Symmetry

I'm folding a protein which is a trimeric long helix bundle.  I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc).  This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves.  I'd like to constrain this to extended conformations only.

I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:

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