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RosettaScript Segmentation Fault (crash log attached)

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RosettaScript Segmentation Fault (crash log attached)
#1

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.

AttachmentSize
ROSETTA_CRASH.log4.02 KB
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Thu, 2020-03-05 07:21
chrisHKL

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.

Thu, 2020-03-05 07:42
jadolfbr

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

Thu, 2020-03-05 09:11
chrisHKL