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LoopModeler mover unable to determine cut point

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LoopModeler mover unable to determine cut point
#1

I am attempting to update my group's GPCR loop modeling protocol to utilize the LoopModeler mover (rather than using the unmaintained LoopRelaxMover as we have been) and am running into errors regarding loop cut points. My XML file is as follows:

<ROSETTASCRIPTS>
    <SCOREFXNS>
    </SCOREFXNS>
    <RESIDUE_SELECTORS>
    </RESIDUE_SELECTORS>
    <TASKOPERATIONS>
    </TASKOPERATIONS>
    <SIMPLE_METRICS>
    </SIMPLE_METRICS>
    <FILTERS>
    </FILTERS>
    <MOVERS>
		<LoopModeler 
			name="loopmodel" 
			config="kic_with_frags" 
			fast="no" 
			auto_refine="yes" 
			>

		<Loop start="147" stop="172" cut="0" skip_rate="0.0" rebuild="yes"/>

		</LoopModeler>
    </MOVERS>
    <PROTOCOLS>
		<Add mover_name="loopmodel"/>
    </PROTOCOLS>
    <OUTPUT />
</ROSETTASCRIPTS>

 

Here is the options file I'm using as well:

#io flags:
-in:file:fullatom
-in:file:s P2Y12_PAR1_LB_ligand_ECL2.pdb
-extra_res_fa VPX.params
-ignore_unrecognized_res true
-cst_fa_file disulf.cst
-cst_fa_weight 1000
-loops:loop_file P2Y12.loops
-loops:frag_sizes 9 3 1
-loops:frag_files P2Y12_9_frag.txt P2Y12_3_frag.txt none 

-loops:remodel perturb_kic_with_fragments
-loops:refine refine_kic_with_fragments

-load_PDB_components false

-out:nstruct 1
-out:pdb
-out:suffix _A

#-run:test_cycles
#-loops:fast

#packing flags
-ex1
-ex2 

-mute core.io.database
-mute protocols.looprelax.FragmentPerturber
-mute core.fragments.ConstantLengthFragSet

-parser
	-protocol nothing.xml
#RosettaEnergyFunction2015
-beta_nov16 true

 

When running the loop modeling job, the following error results:

[ ERROR ]: Caught exception:


File: src/protocols/loops/loops_main.cc:253
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.

 

For some reason, setting the cut value to zero (which should instruct Rosetta to determine a cut point, if I'm not mistaken) isn't working. Pointing the script to a correctly formatted loops file results in the same error. Loop modeling with the LoopRelaxMover using the same input files works fine, am I missing something? I have attached my crash log as well.

AttachmentSize
ROSETTA_CRASH.log5.66 KB
Category: 
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Mon, 2020-06-01 13:12
gszwabowski

Probably not of much help, but in pyrosetta there's a setter method called auto_choose_cutpoint in loop and auto_choose_cutpoints in loops. Maybe this attribute exists for the XML?

Example:

loops = pyrosetta.rosetta.protocols.loops.Loops()
loop = pyrosetta.rosetta.protocols.loops.Loop(i -1,
                                              i + len(addenda_sequence),
                                              0)
loop.auto_choose_cutpoint(pose)
loops.add_loop(loop)

Thu, 2020-07-02 07:27
matteoferla