extract pdbs segmentation fault

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    • September 8, 2017 at 2:20 pm #2739
      Anonymous

        Hey,

        So I ran a docking simulation in which I docked a small molecule to a dimer metal containing protein. I generated 1000 structures output into a  silent file. I wanted the top 10 scoring structures just to see if the run worked and used “grep ‘^SCORE’ IPDock/IPDock.out > IPDock/IPDockScores” to extract scores, the sort command to order them and created a file with the top ten structures.

        The problem arises when I run the extract_pdbs.linuxgccrelease, extract_pdbs.mpi.linuxgccrelease, or extract_pdbs.linuxgccdebug. They fail with a segmentation fault after initializing is completed. I’ve attached a document with the full terminal output of debug as well as the first 100ish lines from the silent file.  I’ve tried including -in:auto_setup_metals also, but that didn’t change anything.

        Any ideas on how to fix this is appreciated, preferably without having to output all structures to pdb.

      • September 8, 2017 at 3:47 pm #13767
        Anonymous

          Sorry for the segfault. A recent code change means that a previously active check is now being bypassed. Thanks for bringing that to our attention.

          But the ultimate reason why you’re getting the error is that you’re missing the commandline parameter to give the params file for your CUR ligand.  Any Rosetta program which deals with your residue needs to get the `-extra_res_fa CUR.params` commandline option, so that it knows how to handle your ligand. Without that, it’s choking because it doesn’t understand what ‘CUR’ is.

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