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Failure in local docking

Submitted by Fei on Thu, 2014-06-26 12:24
Category: 
Docking

Hi all,

I have a set of low resonant protein complex models generated from global docking. I did local docking on each model. Some of them have given the "energy funnel" with its lowest energy structures located around a point, but some don't as the low energy structures are dispersed over the plot, which I guess is a sign of failure in docking. Would this suggest that my starting structures are not good, I mean, not energetically favorable? All these starting models are predicted from XL-mass spec results and a global docking program.

Thanks,
Fei

Post Situation: 
Unsolved
Forums: 
ROSIE - General

Cluster decoys after running PlexPepDock

Submitted by phanvy on Thu, 2014-06-19 06:03
Category: 
Docking

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.

Flags:
-in:file:silent decoys.silent
-database /home/tuongvy/SW/rosetta3.4/rosetta_database
-in:file:fullatom
-score:weights
-score:patch
-cluster:sort_groups_by_energy

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Error when running prepack of PLEXPEPDOCKING

Submitted by phanvy on Wed, 2014-06-18 07:11
Category: 
Docking

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.

Thank!!!

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

-flexpep_prepack
-ex1
-ex2aro

This is the ERROR

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

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

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