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Error when running AqueousPoreFinder protocol

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Error when running AqueousPoreFinder protocol
#1

Hi,

I am currently trying to run a FastRelax protocol for a pore protein (4tsy) with an implicit membrane. To define the membrane I have been using the RosettaMP implementation. However, when running the AddMembraneMover I get the following segmentation fault during the AqueousPoreFinder protocol:

protocols.membrane.AqueousPoreFinder: Initializing a custom aqueous pore boundary
protocols.membrane.AqueousPoreFinder: Writing skeleton ellipse layers to an output file

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

Segmentation fault (core dumped)

 

I have been looking at the output file that is being generated when the segmentation fault occurs but I am unsure of what the format should look like.  All that is written is the following line:

ellipse_no z_loc h k a b r00 r01 r10 r11

 

XML file:

<?xml version="1.0" ?>
<ROSETTASCRIPTS>
  <SCOREFXNS>
    <ScoreFunction name="mpframework_smooth_fa_2012" weights="mpframework_smooth_fa_2012"/>
  </SCOREFXNS>
  <RESIDUE_SELECTORS/>
  <JUMP_SELECTORS/>
  <TASKOPERATIONS/>
  <MOVE_MAP_FACTORIES/>
  <SIMPLE_METRICS/>
  <FILTERS/>
  <MOVERS>
    <AddMembraneMover name="addMembraneMover"/>
    <MembranePositionFromTopologyMover name="init"/>
    <FastRelax name="fastRelax" repeats="5" scorefxn="mpframework_smooth_fa_2012"/>
  </MOVERS>
  <PROTOCOLS>
    <Add mover="addMembraneMover"/>
    <Add mover="init"/>
    <Add mover="fastRelax"/>
  </PROTOCOLS>
  <OUTPUT scorefxn="mpframework_smooth_fa_2012"/>
</ROSETTASCRIPTS>

 

Options file:

-nstruct 10
-parser:protocol ../../xml/4TSYout_relax.xml
-s ../../input_models/4TSYout.pdb
-out:file:silent 4TSYout_relax.out
-out:file:scorefile 4TSYout_relax.sc
-ex1
-ex2
-use_input_sc
-flip_HNQ
-no_optH false
-mp::setup::spans_from_structure true
-relax:constrain_relax_to_start_coords

 

My input structure is obtained from the OPM server (https://opm.phar.umich.edu/proteins/2760) (I cannot upload it because it is too large).

I would appreciate any help!

Many thanks,

Miguel Luengo

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Post Situation: 
Mon, 2023-12-11 02:55
mluengo