Unsolved

I am using the RosettaAntibody3 workflow outlined here: 

Everything is "working" when I use the command:

Dear Rosetta Community,

I am interested in flexible blind/global docking of a monomer to generate homo-dimers. For this I have used the RosettaDock application with -ensemble1 and -ensemble2 flags after passing the prepacked structure to -in file:s. I observe a strong bias in the output population of the docked dimers depending on what I pass in -in file:s. The docking commands are as follows:

Hi all,

I am trying to modify the trRosetta scripts to run it with a ligand (heme; I added few distance constraints between the protein residues and atoms in the ligand).

I ran molfile2params with the -c flag and have both centroid and full atom params and pdb files of the ligand. I inserted the ligand to the pose and converted it to centroid mode for the initial folding calculations. When I add my ligand constraints prior to the minimization stage, after all the network constraints are read, I get the following error:

Hi everyone,

        I have some problems about protein and protein docking. I want to dock a peptide into protein using global docking. But there are some carbohydrates in my protein. After docking, the site of the protein bonds with carbohydrate and the carbohydrates bond each other have some error. And the score of the results are very high.

Generally, they should automatically dehydrogenate after docking. Did I miss some commands or how can I solve this problem?

I attach the output's image and following is my flag: