# Constraints

## calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

Category:
Structure prediction
Constraints
Symmetry
Membrane

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.

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## FlexPepDock bug? Constraints do not appear in total_score?

Category:
Constraints

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

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## 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:

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## 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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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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## 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: