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AddMembrane Mover Segmentation Fault

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AddMembrane Mover Segmentation Fault
#1

Hello,

I am using Recon MSD. I have run it functionally for a few months but now it is not working. When I try to run my bash script I get an error at the same point every time. It is during the "AddMembrane" step of my Rosetta Scripts protocol. I have tried countless tweaks to my inputs and my scripts but the same segmentation fault happens at the same time every run. 

ESC[0mcore.util.switchresiduetypeset: (0) ESC[0mESC[1m[ WARNING ]ESC[0m When swi
tching to a fa_standard ResidueTypeSet:  Pose already contains fa_standard Resid
ueTypes.
ESC[0mprotocols.DsspMover: (2) ESC[0mLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHH
HHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHLLLLLLH
HHHHHHHHHHHHHHHHHHHHHHHHHLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHH
HHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHLLLLLL
ESC[0mprotocols.membrane.MPLipidAccessibility: (2) ESC[0mnbeta: 0 nmem: 98 beta:
 0
ESC[0mprotocols.DsspMover: (1) ESC[0mLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHH
HHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHLLLLLLH
HHHHHHHHHHHHHHHHHHHHHHHHHLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLHHHHHHHHHHHHHHHHHHHHLLLLLL
ESC[0mprotocols.membrane.MPLipidAccessibility: (1) ESC[0mnbeta: 0 nmem: 106 beta: 0
ESC[0mprotocols.membrane.MPLipidAccessibility: (2) ESC[0m-15.351 15.351 10.234 6 10
ESC[0mcore.membrane.hull: (2) ESC[0mconcave shell
ESC[0mprotocols.DsspMover: (0) ESC[0mLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLHHHHHHHHHHHHHHHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLHHHHHHHHHHHHHHHHHHHHLLLLLL
ESC[0mcore.membrane.hull: (2) ESC[0mconvex hull
ESC[0mprotocols.membrane.MPLipidAccessibility: (0) ESC[0mnbeta: 0 nmem: 103 beta: 0
ESC[0mprotocols.membrane.MPLipidAccessibility: (1) ESC[0m-15.351 15.351 10.234 6 10
ESC[0mcore.membrane.hull: (1) ESC[0mconcave shell
ESC[0mcore.membrane.hull: (1) ESC[0mconvex hull
ESC[0mprotocols.membrane.MPLipidAccessibility: (0) ESC[0m-15.351 15.351 10.234 6 10
ESC[0mcore.membrane.hull: (0) ESC[0mconcave shell
ESC[0mcore.membrane.hull: (0) ESC[0mconvex hull
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
------------------------------------------------------------
A process or daemon was unable to complete a TCP connection
to another process:
  Local host:    tnxt-0447
  Remote host:   tnxt-0463
This is usually caused by a firewall on the remote host. Please
check that any firewall (e.g., iptables) has been disabled and
try again.
------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 0 on node tnxt-0447 exited on signal 11 (Segmentation fault).

 

My inputs:

Spanfile

TM region prediction for start predicted using OCTOPUS
8 240
antiparallel
n2c
   3    28
  35    58
  65    87
  96   117
 127   148
 159   178
 185   209
 216   236

 

My PDB:
Attached, all three states are same protein in slightly different conformation. 

My Script:

            <ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="ref15" weights="ref2015" />
                <ScoreFunction name="memb_hires" weights="mpframework_smooth_fa_2012" />
        </SCOREFXNS>
        <TASKOPERATIONS>
                <SeqprofConsensus name="pssm" filename="pssm.txt" probability_larger_than_current="true" />
                <InitializeFromCommandline name="ifcl" />
 <ReadResfile name="resfile" filename="resfile.txt"/>
        </TASKOPERATIONS>
        <MOVERS>
                <AddMembraneMover name="add_mem" spanfile="handjam.span" />
                <MembranePositionFromTopologyMover name="init_pos" />
                <PackRotamersMover name="design" scorefxn="memb_hires" task_operations="ifcl,resfile,pssm"/>
                <Backrub name="backrub_man" pivot_residues="1-239" />
                <GenericMonteCarlo name="backrub" mover_name="backrub_man" scorefxn_name="memb_hires" trials="50" temperature="0.8" recover_low="1" />
                <MSDMover name="msd1" design_mover="design" post_mover="backrub" constraint_weight="0.5" resfiles="resfile.txt" debug="1" />
                <MSDMover name="msd2" design_mover="design" post_mover="backrub" constraint_weight="1.0" resfiles="resfile.txt" debug="1" />
                <MSDMover name="msd3" design_mover="design" post_mover="backrub" constraint_weight="1.5" resfiles="resfile.txt" debug="1" />
                <MSDMover name="msd4" design_mover="design" post_mover="backrub" constraint_weight="2.0" resfiles="resfile.txt" debug="1" />
                <FindConsensusSequence name="finish" scorefxn="memb_hires" resfiles="resfile.txt" task_operations="ifcl" />
        </MOVERS>
        <FILTERS>
                <FitnessFilter name="fitness" output_to_scorefile="1" />
        </FILTERS>
        <PROTOCOLS>
                <Add mover="add_mem" />
                Add mover="init_pos"
                <Add mover="msd1" />
                <Add mover="msd2" />
                <Add mover="msd3" />
                <Add mover="msd4" />
                <Add mover="finish"/>
                <Add filter="fitness"/>
        </PROTOCOLS>
        <OUTPUT scorefxn="ref15" />
</ROSETTASCRIPTS>

Any idea of where I can check/tweak my inputs would be greatly appreciated. 

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Post Situation: 
Thu, 2022-04-14 14:02
csvajda