high-res docking

[Anonymous]

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!

[Anonymous]

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.

[Anonymous]

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?

[Author]

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