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
Attachment | Size |
---|---|
Rosetta crash log | 4.93 KB |
Spanfile generated from pdb strucuture | 153 bytes |
Complete rosetta output | 21.57 KB |
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