constraint are not imposed during protein-ligand docking

[Anonymous]

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

 

Could you help me wiht this issue? why aren’t the constraints used? I do not get any errors, but the output does not meet the constraints.

Thank you

[Anonymous]

If you’re using RosettaScripts, then constraints will not be automatically loaded. You’ll have to load them explicitly with a mover like the ConstraintSetMover. In addition, the -constraints:cst_weight option won’t automatically add constraints for the scorefunction. Instead, you’ll need to add them manually in the Scorefxn block, or use a weights file with them added. If you have constraints loaded into the pose and the terms enabled in the scoring function, then they should be obeyed.

For ligand docking, I believe that the recommended ligand weights files already have relevant constraint terms turned on. (Though at a weight of 1.0, rather than 10.0).

The one complication is that the TransformMover from ligand docking doesn’t use a standard Rosetta scorefunction. As such, it doesn’t obey constraints by default. However, recent versions of Rosetta have options on the TransformMover which allow you to enable constraints (the use_constraints and cst_fa_file in the documentation for TransformMover).

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