Using antibody_designer to graft loops on one CDR. I'd like to fix the sequence of the grafted loop to native. It appears to ignore the
I have tried something like this in my cdr_instruction file
H3 GraftDesign ALLOW
ALL SeqDesign FIX
I've also tried passing it a resfile forcing everything to be native like so
But, it does not seem to follow this. Does NATAA in the context of grafting mean that use native sequence of cdr being grafted? Or, is NATAA just being ignored in the context of grafting?
I've even tried manually listing out the positions that will be grafted in the resfile and explicitly giving the desired AA identity. This throws an error saying one of the positions I specified was not in the pdb even though it is in the input pdb. Is there some renumbering going on here during grafting? I did renumber the pdb to the AHo scheme before running antibody_designer. Also, I am keeping the loops the same length as native, so I would not expect renumbering.