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Cluster decoys after running PlexPepDock


Hello everone

After running the Plexpepdock, I have 40000 decoys. I try to use the cluter program of Rosetta 3.4 . But, I do not understand the meaning of cluster. Because , after I tried to run with 200 decoys and get the out:file with 200 file c.0.XXX.pdb format. I do not understand how cluster work.

-in:file:silent decoys.silent
-database /home/tuongvy/SW/rosetta3.4/rosetta_database

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Error when running prepack of PLEXPEPDOCKING


Hello everyone!
I use Plexpepdocking (Rosetta 3.4), in my structure have one ion Zn , but Plexpepdock can not recognize it.
Please take a look on my pdb file and tell me how to fix this Error.
Thank you so much for your help.


this is the flag for pre_packing
-s tryzn.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database


This is the ERROR

ERROR: unknown atom_name: ZN CA
ERROR:: Exit from: src/core/chemical/ line: 1692

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Docking protein complexes when constrained by oligomer symmetry


I am currently trying to set up a docking run between two proteins that have compatible symmetry, and almost certainly interact along a 3-fold symmetry axis. One molecule is trimeric, the other is a D3 hexamer, with protomeric MWs of 20 and 25 kDa respectively. I have experimental (x-ray) structures for both proteins, and an initial model where the two proteins are in contact, and lined up with the 3-fold axis of each along Z. I therefore want to search only rotations around Z, along with a small Z-translation shift.

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