Docking

Good afternoon. I would like to run the full protein-protein docking protocol, but i have my structures in two separate pdbs and the input structure is a single pdb with both structures. What can i do?

Hello,

I have recieved this warning when trying to use FlexPepDocking refinement protocol for a tyrosine phosphorylated peptide.

core.util.switchresiduetypeset: (0) [ WARNING ] When switching to centroid mode, a normal replacement type for residue TYR:phosphorylated can't be found.

core.util.switchresiduetypeset: (0) [ WARNING ]     an autogenerated replacement type is being used instead.

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 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: