I'm following the antibody modeling protocol recently published in Nature Protocols "Modeling and docking of antibody structures
with Rosetta". I run into an error when running snugdock with ensembles. I get a segfault (last couple lines posted) with no additional info. However, if I don't specify to run with ensembles, the snugdock run proceeds to completion. I'm using rosetta3.8.
tail of output:
protocols.docking.DockingLowRes: /// Ensemble 1: on ///
protocols.docking.DockingLowRes: /// Ensemble 2: on ///
protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::
Segmentation fault (core dumped)
Here's my flags file:
#-partners LH_ABD # Tried with and without this
-ensemble1 ensemble_antibody.list # removing these two lines will make it work
# rotamer settings
I've attached my full log file. My ensemble lists contain full paths to all structures (indeed, they seem to be correctly read based on the log file).
Any ideas what could be going wrong?