I am new to Rosetta design. I am currently using Flex_ddG to design a peptide that will have a higher binding affinity than the native peptide substrate of a certain protease. I have both the coordinates of the receptor (chain A) and the peptide (chain C) in a single pdb file. I ran the program per instruction, and it works if my chain_to_move.txt file specifies only one chain (e.g. "A" OR "C"). However, if I attempt to specify both chains (i.e, "A,C") the program crashes, and it spits out this error: "InterfaceDdGMover needs to have chains (numbers or names) or jumps defined to move"
I hope somebody can help. Thank you!