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Cluster decoys after running PlexPepDock

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

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Error when running prepack of PLEXPEPDOCKING

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

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Docking protein complexes when constrained by oligomer symmetry

Category: 
Docking

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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Error 500 Docking protein

Category: 
Docking

Dear all,
I have submitted a couple of protein-protein docking (docking2) jobs.
I have received the confirmation mails but the results aren't accessible, even if i can see them in my queue list as "Finished". I Suppose they are not failed aas i would expect a "Failed" status, but i got this "Error 500 - We're sorry but we weren't able to process this request." reply.

How can I fix it?

Thank you

Andrea Coletta (Sherpaman)

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Ligand docking: ERROR: set_atom_base: atoms must be bonded!

Category: 
Docking

Hi,
I'm new in rosetta docking. I ran this command
/farm/software/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -database /farm/software/rosetta3.5/rosetta_database/ -run:constant_seed -run:rng mt19937 -overwrite -no_optH -ex1 -ex1aro -ex2 -mute core.util.prof -mute core.io.database -run:preserve_header -in:file:s RCL+LMP.pdb -extra_res_fa LMP.fa.params -extra_res_cen LMP.cen.params -parser:protocol ligand_dock_LMP.xml -enzdes:cstfile LMP.cst -nstruct 3 > output.log
and it was stopped by
ERROR: set_atom_base: atoms must be bonded!

Post Situation: 

Ligand docking: ERROR: set_atom_base: atoms must be bonded!

Category: 
Docking

Hi,
I'm new in rosetta docking. I ran this command
/farm/software/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -database /farm/software/rosetta3.5/rosetta_database/ -run:constant_seed -run:rng mt19937 -overwrite -no_optH -ex1 -ex1aro -ex2 -mute core.util.prof -mute core.io.database -run:preserve_header -in:file:s RCL+LMP.pdb -extra_res_fa LMP.fa.params -extra_res_cen LMP.cen.params -parser:protocol ligand_dock_LMP.xml -enzdes:cstfile LMP.cst -nstruct 3 > output.log
and it was stopped by
ERROR: set_atom_base: atoms must be bonded!

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