I am trying to dock two proteins but I keep getting this error. I am not sure why its there as there are two chains in the pdb.
Can anyone help?
It looks like you're separating the two chains with an ENDMDL tag. By default Rosetta will only read the first model of a multi-model file, so you're only getting the first chain.
Change the ENDMDL lines to TER lines, and you should be good.
Fantastic, thank you!