Category:
Docking
Hello:
After low-res docking,I'm going to do high-res protein/protein docking.There are two modes(High Resolution Docking Only;High Resolution Docking minimization)in the rosetta3.4 user guide.Which one should I choose?
Here is my flags:
1.High-res docking only flags
-s 1.pdb
-partners ABC_DE
-ex1
-ex2aro
-use_input_sc
-docking_local_refine
-nstruct 1000
-mute core.util.prof
-out:overwrite
-out:pdb
-mute core.io.database
2.High-res docking minimization flags
-s 1.pdb
-partners ABC_DE
-ex1
-ex2aro
-use_input_sc
-docking_local_refine
-dock_min
-nstruct 1000
-mute core.util.prof
-out:overwrite
-out:pdb
-mute core.io.database
Thank you very much!
Post Situation:
Hi Tfliu!
-dock_min flag does a single round of minimization in high resolution, skipping the mcm protocol. So if you want mcm protocol use the first set of flags.
Thanks for kind comments!
In the high-res docking,I use high-res docking only flags to repack sidechains followed by high-res docking minimization to minimize the energy of the rigid body position.Does this make sense?
Also,is there something wrong with my high-res docking minimization flags?