I am trying to run fixbb on a heterodimeric protein and explore different residues at 2 different positions in one chain. The program runs without error however all the structures output (100) have the native residues at those 2 positions. My .resfile and flags are below.
EX 1 EX 2
72 A NOTAA C
79 A NOTAA C
Which executable are you running (fixbb)? What is the native residue type? Design with only two mutable residues and no mobile residues will converge nearly perfectly, so it may just be that Rosetta thinks the native sequence is best – try adding “NOTAA CX” where X is the native type to force mutations. You should almost certainly be using NATAA not NATRO for your global settings (repack without designing) and probably also use EX 1 EX 2 on your 72 and 79 lines to get extra rotamers for those positions, like so:
NATAA EX 1 EX 2 USE_INPUT_SC
72 A NOTAA Cx EX 1 EX 2 USE_INPUT_SC
79 A NOTAA Cx EX 1 EX 2 USE_INPUT_SC
Yes I am running the fixbb executable. The native residue at position 72 is Val while that at 79 is ALA. I will try your suggestions. It did occur to me that that the native residues are best but I was expecting some other combinations to be there also. If I am excluding the native residue, do I need to add “USE_INPUT_SC” on each line?