I am running a docking_protocol for two proteins. Inspecting the score.sc file, I find that the columns Fnat and Irms are "nan" (Not A Number, I suppose). Why could this be happening? I can post more details if needed.
(BTW, what does Fnat mean?)
I just realized that the starting pdb I am using to run the docking simulation has both protein chains separated, which means that the initial structure has no interface. So that explains why Irms is nan (right?).
So that leaves Fnan. What does it mean and why is it also NaN?
"Fnat" is the fraction of native contacts recovered. ("Contact" here being residues within 5 Ang of the binding partner.)
If you don't have an interface, there are no native contacts, so to compute the fraction of native contacts you would divide by zero ... resulting in the observed not-a-number (nan) value.