RosettaScript Segmentation Fault (crash log attached)

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    • #3367
      Anonymous

        The following is my .xml script:


        <ROSETTASCRIPTS>

        <TASKOPERATIONS> You can control which parts you want to change from here

        <ProteinInterfaceDesign name="pido" repack_chain1="1" repack_chain2="1" design_chain1="0" design_chain2="1" interface_distance_cutoff="7"/> task operation that designates which residues are designable and repackable at the interface
        </TASKOPERATIONS>

        <RESIDUE_SELECTORS>
        <Chain name="chB" chains="B"/>
        </RESIDUE_SELECTORS>

        <SIMPLE_METRICS>
        InteractionEnergyMetric name="interface_energy" scoretypes_only="talaris2014"
        <RMSDMetric name="rmsd" rmsd_type="rmsd_all" residue_selector="chB" use_native="true"/>
        <TotalEnergyMetric name="total" residue_selector="chB"/>
        <TimingProfileMetric name="clock"/>
        </SIMPLE_METRICS>

        <MOVERS>
        <MutateResidue name="D63A" target="63A" new_res="ALA"/>
        <MutateResidue name="E64A" target="64A" new_res="ALA"/>
        <MutateResidue name="E67A" target="67A" new_res="ALA"/>

        <RepackMinimize name="des1" scorefxn_repack="soft_rep" scorefxn_minimize="soft_rep" minimize_bb_ch1="0" minimize_bb_ch2="1" minimize_rb="0" task_operations="pido"/> This works
        <RepackMinimize name="des2" scorefxn_repack="talaris2014" scorefxn_minimize="talaris2014" minimize_bb_ch1="0" minimize_bb_ch2="1" minimize_rb="0" task_operations="pido"/> This works
        <RunSimpleMetrics name="metric1" metrics="clock,rmsd,total" prefix="m1_"/>
        <RunSimpleMetrics name="metric2" metrics="clock,rmsd,total" prefix="m2_"/>
        <ParsedProtocol name="design">

        <Add mover_name="des1"/>
        <Add mover_name="des2"/>
        </ParsedProtocol>
        <GenericMonteCarlo name="iterate" scorefxn_name="talaris2014" mover_name="design" trials="3"/> Iterate through design to find best solution. change trial numbers to higher for real application.
        </MOVERS>

        <PROTOCOLS>
        <Add mover="D63A"/>
        <Add mover="E64A"/>
        <Add mover="E67A"/>
        <Add mover="metric1"/>
        <Add mover="iterate"/>
        <Add mover="metric2"/>
        </PROTOCOLS>
        </ROSETTASCRIPTS>

         

        And my flags are:


        -s 200ns1-101_AB.pdb
        -restore_talaris_behavior
        -ex1
        -ex2
        -packing:linmem_ig 10
        -extrachi_cutoff 5
        -ignore_unrecognized_res
        -nstruct 1000
        -jd2:ntrials 1
        -parser:protocol updated2-notree.xml
        -docking:no_filters
        -out:file:silent bin_struct.o
        -in:file:native 200ns1-101_AB.pdb
        -in:file:fullatom

         

        Rosetta is crashing after the “iterate” mover finishes and during the “metric2” mover like so:



        protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER RunSimpleMetrics - metric2=======================
        protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: TimingProfileMetric - calculating timing_profile
        protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: RMSDMetric - calculating rmsd


        AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

         

        Crash log is attached and any insight would be appreciated. Thanks.

      • #15201
        Anonymous

          You are using rmsd_all – for ALL heavy atoms – but you are doing design. Usually, we are pretty robust about skipping atoms that don’t match, but that is not garunteed.  I would use CA or BB.  I would also update your Rosetta to a newer release.  I know I fixed a bug in the RMSDMetric superposition over the past few months.  Not sure if that is what you are seeing here, but I would still update.

          • #15202
            Anonymous

              Thank you, switching it to BB resolved the issue. But yes, I will also update the program

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