Constraints

Loop modeling with constraints

Category:
Loop Modeling
Constraints

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]

[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:

Post Situation:

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:
"

Post Situation:

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.

Post Situation:

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

Post Situation:

using full atom constraint in docking

Category:
Constraints

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

Post Situation:

minimize_with_cst and convert_to_cst_file for ddG_monomer issues/confusion

Category:
Constraints

Generating Constraints File and Pre-Minimization Problems with ddG_Monomer Application -

Hello,

Post Situation:

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.

Post Situation: