Hello,
I am attempting to use the GALigandDock mover to perform dockings of a metal ligand similar to heme. I am following this paper: https://pubs.acs.org/doi/suppl/10.1021/jacs.3c02742/suppl_file/ja3c02742_si_001.pdf.
I generated a params file using the molfile_to_params script, and proceeded to use the exact same command and docking xml file.
However rosetta_scripts routinely segfaults around 3.5 minutes. Is this because I am using the normal params file and not a generic potential params file? I tried using the generic potential mol2_params however I could not get the script to run, it also errors.
When I switch out my ligand that has a metal for a regular organic ligand I do not have this segmentation fault occur.
If the problem is that my ligand has a metal in it then how could I get around this issue? In the paper they are docking heme which has an iron as well so I believe this should have worked.
Thank you!
This is the mol2_params script error:
failed on generating params file for TAM.mol2
Traceback (most recent call last):
File "/home/research/rosetta/main/source//scripts/python/public/generic_potential/mol2genparams.py", line 138, in main
run_mol2(mol2file,option)
File "/home/research/rosetta/main/source//scripts/python/public/generic_potential/mol2genparams.py", line 46, in run_mol2
molecule = MoleculeClass(mol2file,option)
File "/home/research/rosetta/main/source/scripts/python/public/generic_potential/Molecule.py", line 121, in __init__
stat = self.read_mol2()
File "/home/research/rosetta/main/source/scripts/python/public/generic_potential/Molecule.py", line 187, in read_mol2
self.name = words[0]
IndexError: list index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/research/rosetta/main/source//scripts/python/public/generic_potential/mol2genparams.py", line 154, in <module>
main(option)
File "/home/research/rosetta/main/source//scripts/python/public/generic_potential/mol2genparams.py", line 145, in main
run_mol2(mol2file,option)
File "/home/research/rosetta/main/source//scripts/python/public/generic_potential/mol2genparams.py", line 46, in run_mol2
molecule = MoleculeClass(mol2file,option)
File "/home/research/rosetta/main/source/scripts/python/public/generic_potential/Molecule.py", line 121, in __init__
stat = self.read_mol2()
File "/home/research/rosetta/main/source/scripts/python/public/generic_potential/Molecule.py", line 187, in read_mol2
self.name = words[0]
IndexError: list index out of range
The seg fault always occurs after this:
protocols.ligand_docking.GALigandDock.GridScorer: Building 117 x 117 x 117 grid; origin = ( -15.3124,-6.64478,-20.9294 )
protocols.ligand_docking.GALigandDock.GridScorer: maxdis = 7.51668
protocols.ligand_docking.GALigandDock.GridScorer: subhash_buffer = 0.866025
protocols.ligand_docking.GALigandDock.GridScorer: hash_grid = 8
protocols.ligand_docking.GALigandDock.GridScorer: Calculating gridded energies for 27 unique atom types
protocols.ligand_docking.GALigandDock.GridScorer: and lkb virtual parameters for 12 unique polar atom types
protocols.ligand_docking.GALigandDock.GridScorer: Grid calculation took 21.6696 seconds.
The Crash file looks like this:
##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#
[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:52:25.363712
[APPLICATION]: /share/apps/rosetta/bin/rosetta_scripts
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-39)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-in:file:s=complex.pdb -in:file:extra_res_fa=TAM.params -parser:protocol=script -packing:ex1 -packing:ex2 -corrections:beta -corrections:gen_potential
[END_OPTIONS]
[START_BACKTRACE]: RAW_LIBC
[0x6470cac]
[0x6bf3950]
[0x5ee819c]
[0x5f0ce08]
[0x5f0d2e0]
[0x49143b5]
[0x1c589be]
[0x1c6f77a]
[0x3acbc2a]
[0x3acc9f4]
[0x3acd50e]
[0x3b68eec]
[0x3b6ab11]
[0x3c06ba8]
[0x41976e]
[0x6beae64]
[0x6beb0e1]
[0x651b96]
[END_BACKTRACE]
[FILE]: SIGSEGV
[LINE]: 11
[START_MESSAGE]
Segmentation Fault
[END_MESSAGE]
[END_CRASH_REPORT]