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.