I am trying to design a 2 fold-symmetrical protein where I want to design a selected number of residues in each half and not mutate the remaining residues in both the halves. For e.g., what I want Rosetta to do is in "Half-A, the residues at position 32, 49, 56, 65, 66 should be mutated to certain residues, and the exact same mutated residues should appear after designing position 32, 49, 56, 65, 66 in Half-B.
I found that the Rosetta LinkResidues can do it. So, I tried to write a Rosetta Script with all the necessary information from the LinkResidues page of Rosetta. Note: I took into consideration the suggestions for possible bugs to avoid Segmentation fault.
But when I run my script with my resfile and flags files, I am getting "Segmentation fault (core dumped)" error without any further information.
I am attaching all the files and scripts that I have used. If any expert can help me in resolving this probelm, that would be really helpful!
Script I am using
<ReadResfile name="resfile" filename="my_resfile.res"/>
<PackRotamersMover name="packer" scorefxn="talaris2014" task_operations="resfile,linkres"/>
Runs movers and filters in this order
I can't answer your question, but I share your frustration with the link residue system. I created a task operation that replaces the residue linking for simple systems (see link below) but it looks like it won't help your case. Are you comfortable running a debugger like GDB to provide a backtrace when the program segfaults?