You are here

debug rosetta_scripts FunFolDes run

2 posts / 0 new
Last post
debug rosetta_scripts FunFolDes run

I'm running a FunFolDes and it works for one protein, but outputs segmentation fault on other three. I checked all the proteins contain standard amino acids, no cys.

Admin installed debug version on our cluster and said to run ml rosetta/2019.14.debug, but i can't find anywhere how to run debug version.

i was running 

/rosetta_scripts -parser:protocol fold_design.xml -in:file:s 1mhx.pdb -out:nstruct 65 -in:ignore_waters -in:ignore_unrecognized_res -beta -ignore_zero_occupancy 0 -out:file:silent_struct_type binary -out:prefix ${SLURM_ARRAY_TASK_ID}_1mhx_ -out:file:silent 1mhx_silent_${SLURM_ARRAY_TASK_ID}_ -parser:script_vars frags=frag_1

Attached example of log run during normal run.

with what parameters and how should debug version be run?

thank you!


output.34044702_18.log44.03 KB
Post Situation: 
Sun, 2019-08-18 23:17
    <Index name="template" resnums="8A-65A" /> 

Face the same issue and find that the segmentation fault comes from this line. Changing the index residue selector to 

<Chain name="template" chains="A" /> 

makes the fault go away but of course then design operates on the whole chain instead of the selected part. Not sure why this. Shouldn't Index and Chain residue selectors do the exact same thing. 

Wonder if you managed to find a solution to the segmentation fault issue?

Wed, 2020-11-18 05:47