I did a global docking of two proteins followed by a refinement run. Then I performed MD refinement on the docked complex (50ns using gromacs). What I'd like to do is compare the interface energies of my docked complex before and after MD. What I specifically want is for Rosetta to write the section "Pair energies across interface" of my post MD pdb file, just like it does for all docking decoys generated. I've tried launching Rosetta with the -score flag i.e.:
rosetta.gcc -score -s file.pdb -nstruct 1 -scorefile filescored
When I view the output pdb; file_001.pdb, it is scored but I'm expecting to see the pair energies scoring section, which isn't there. Another thing I noticed is that this output file only includes chain C of my complex, where the pdb file is formatted as follows:
I suspect that rosetta can't read properly read my pdb to find an interface (it only sees chain C) or, I'm missing a flag. Is it possible to do what I want using the -score mode of rosetta, or is there another way to accomplish what I'm asking?
I also see that there was a similar question asked earlier, and the response was to do a docking rather than using the -score flag. If I must use the -dock flag, what other flags would I use to assure that Rosetta doesn't alter (perturb) my starting structure at all?
Thanks for your help.