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Docking

docking2: local_docking vs docking_local_refine

Submitted by AdoCbl on Sat, 2015-08-08 23:57
Category: 
Docking

When I submit ROSIE docking2 jobs at http://rosie.rosettacommons.org/docking2/submit
there are options for local_docking and docking_local_refine docking protocols.
What is the difference between these options?
Where can I find documentation about them?

Thanks!

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ROSIE - General

How to judge docking success for two proteins without knowledge of native structure

Submitted by jasnyderjr on Fri, 2015-07-10 14:27
Category: 
Docking

If you are trying to dock two proteins, using a global search, with no knowledge of correct answer (native structure) , how does one judge a docking success?. When reporting benchmark results, for example, the native (or mock-native) structure is used to rmsd against, and the definition of docking funnel is based on I_rmsd, so judgement of docking success is always based on some known (native) structure (or correct answer). Starting with just two proteins arbitrarily place apart.

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Rosetta 3 - General

Cancel / delete Rosie not working

Submitted by fglaser on Tue, 2015-07-07 01:14
Category: 
Docking

Hi,

I am trying to Delete / Cancel jobs on Rosie that I suspect will fail, so I want to save running time and send another job.

But when I click on the Delete / Cancel links on my account fglaser_rosie, nothing happens....

What I am doing wrong?

Best regards,

Fabian
Technion, Haifa
Israel

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ROSIE - General

Job 「№15623」has failed

Submitted by fglaser on Tue, 2015-07-07 00:17
Category: 
Docking

Hi

Iam a newby with Rosie, I sent a PDB and sdf file with many molecules for Rosie docking, and I got the following input error message:

Job 「№15623」has failed with the message:

molfile_to_params step failed, please double check your input files!

I searched the documentation and for what I know the input PDB and the SDF where in correct format, but of course I maybe wrong...

Could you please explain me what exactly is wrong with the input and how to correct it?

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ROSIE - General

nbr_atom in ligand docking

Submitted by phanvy on Fri, 2015-07-03 07:40
Category: 
Docking

Dear all,
I run ligand docking protocol to dock a small chemical on my protein.
I set up the inital position of ligand is "-start_from 1.36 50.07 23.4".
Follow the document, the nbr_atom of the ligand is chosen near the inital position of ligand. But when I check the log file, I saw the nbr_atom of the ligand is far away from the inital position of ligand: 44.03500058226830 112.4592971897935 22.25074880071337
4.886590717968414 0.06526207982382815 17.92231676318689

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Rosetta 3 - General

the output of ligand docking

Submitted by phanvy on Fri, 2015-07-03 01:27
Category: 
Docking

Dear all,
I run the ligand docking protocol to dock a small chemical to protein.
this is my flag
-packing
-no_optH
-ex1
-ex1aro
-ex2
-docking
-dock_pert 30 5
-ligand
-improve_orientation 1000
-minimize_ligand
-harmonic_torsions 10
-minimize_backbone
-harmonic_Calphas 0.3
-soft_rep
-old_estat
-start_from 1.36 50.07 23.4
-protocol abbrev2

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Rosetta 3 - General

RosettaProtein_Docking

Submitted by khadkab@mcmaster.ca on Tue, 2015-06-30 11:28
Category: 
Docking

Hi Everyone, I was wondering if anyone knows how to set path for saving output pdb files in Rosetta protein docking. I was using following command line to run protein docking, didn't found any saved output pdb files.

/path to/rosetta_2014.35.57232_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug @docking.options -parser:protocol docking_full.xml -database /path to/database/ -out:suffix _full -nstruct 50 > docking_full.log -restore_pre_talaris_2013_behavior

Docking.option file

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Rosetta 3 - General

docking with constraints and flexible bb

Submitted by mintseris on Mon, 2015-06-22 09:07
Category: 
Docking
Loop Modeling
Constraints

Hi,
I am doing unbound docking and i believe I have enough biological info to locate the binding interface and rough orientation. Doing the docking manually (or with the low res protocol) suggests that there's some conformational change in the interface that I would like to model. I'm guessing this is not something that I can accomplish with the old docking_protocol commandline app. I did see a flexible_bb_docking option but that appears to be undocumented? Maybe I can do this via the ensembles options?

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Rosetta 3 - Applications

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