I have been getting an error which says that "The native pose does not have jump number 2”.. What should i do in this case? please help me!
Most Rosetta applications assume that the native you're comparing to matches up with the complex you're docking. That error message indicates that you're docking over jump 2 (that is, you're docking the third chain) in your input structure, and Rosetta is looking for the corresponding jump 2 (that is, the third chain) in the native structure.
From the error message, I surmise that you only have two chains in the native structure. Are you missing a cofactor in your native, or is there some other difference (a chainbreak, perhaps) that's present in your input structure but not in your native structure (or vice versa)?
Another thing you can try is updating to a more recent version of Rosetta. (I don't think it's in Rosetta 3.8, but it should be in the most recent weekly releases). The way the ligand was identified changed internally, such that the ligand is matched on chain letter, rather than jump number. This way it shouldn't matter if there are more/fewer spurious chains (e.g. cofactors) in your native/input - as long as the ligand to be compared is the same PDB chain letter (e.g. 'X'), it should work. (Emphasis on *should*.)
Note that if you don't have a native structure you're interested in getting a comparsion to, you can probably omit the native completely from your input files (e.g. remove the `-in:file:native` specification from your commandline.) The only thing the native is used for is a reference for rmsd calculations - you should be able to omit it and still get identical docking results.