Member Site Forums Rosetta++ Rosetta++ – General How to dock structures locally? Reply To: How to dock structures locally?


    Hi Here is the suggestions I got from one of the docking developers.

    use pose docking instead of regular docking in rosetta++. This can be done simply by adding “-pose” to the command line. I ran this command line with “-pose” and without “-pose” and in normal docking, dock_pert 0 0 0 does indeed create some decoys that are significantly perturbed from the starting structure. I did not see this when using pose docking.

    > I am trying to perform a local protein docking. The two docking partners are 5 A away from the native complex. What would be te right command to dock these structures locally. I tried to set the -dock_pert flag to 0 0 0. This still resulted in large numbers of decoys that where rotated with more than 80 degrees and translated more than 10 A.
    > This is the command I used:
    > rosetta AA 0001 _ -dock -dock_mcm -dock_rtmin -dock_pert 0 0 0 -s 0001.pdb -nstruct 200
    > Thanks,