Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › RosettaScript Segmentation Fault (crash log attached)
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March 5, 2020 at 3:21 pm #3367Anonymous
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:fullatomRosetta 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.
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March 5, 2020 at 3:42 pm #15201Anonymous
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.
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March 5, 2020 at 5:11 pm #15202Anonymous
Thank you, switching it to BB resolved the issue. But yes, I will also update the program
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