I want to redesign the interface of two three-fold symmetrical proteins and I thought of using RosettaScripts.
I first wanted to make it work on one three-fold symmetrical protein and then continue with the interaction, but I am stumbling on some errors.
I'm using LinkResidues, because the protein is three-fold symmetrical, so a mutation on residue a should also occur on residue b and c, thus without breaking the symmetry of those residues.
<ReadResfile name="int_one" filename="int_one.txt" />
<LinkGroup group="a,b,c" />
<LinkGroup group="d,e,f" />
<LinkGroup group="g,h,i" />
<LinkGroup group="j,k" />
<ExtraRotamersGeneric name="extrachi" ex1="1" ex2="1" ex1_sample_level="4" ex2_sample_level="4" />
There is no residue l, due to the N-, C-terminal stuff, so j and k are just linked together.
Via Movers I do the "PackRotamersMover" and select all three (int_one, IntDesign, extrachi) and via protocol I do "Add mover".
The ResFile 'int_one.txt' contains residues a-k, all on separate lines with the correct chain and 'PIKAA' followed by the amino acids I prefer (a few just have one option, but I thought that's okay normally).
When I excecute this I get a 'segmentation fault'-error, but if I remove one '<' of the LinkGroups or keep the script intact but just remove one residue (i.e. "d,f" instead of "d,e,f" it will work.
I also tried to have one residue outside the linked residues that is also allowed to be mutated via an extra PackRotamersMover function, but that didn't change the 'segmentation fault'-error.
Can anybody help/explain this problem please?
Thanks in advance!