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Docking

Checkpoint with rosetta3.4

Category: 
Docking

Hello,

I would like to use checkpoints in order to restart a job if it ends because of a wall-time before he finishes.
I tried the flags:
-in:file:checkpoint true
-run:checkpoint true

But no file is generated, it doesn't look to work.
Anyone knows how I can use checkpoint in the docking protocol?

Thanks

Amélie

Post Situation: 

Docking2: Mismatch between score file and graph

Category: 
Docking

When looking at the graphical docking output (Interface score I_sc / RMSD) the values shown when hovering over the dot do not match the values on the graph itself (see screenshot, ScoreGraph.png). The lowest scoring decoy has a I_sc of ~-6 while the value shown is -4.5. The numbers of the decoy do not match either, the lowest scoring decoy from the result list is 0927 and has a I_sc of -6.228 (which would fit the graph), but on the graph the number is 0836. In another run the values and numbers matched.

Post Situation: 

Docking flags

Category: 
Docking

Hi all,

I'm trying to change the filters for the docking protocol.
I tried :
dock_lowres_filter 15 5
This option is supposes to set manually the interchain_contact and the interchain_vdw cutoff.

However my log file still says that the cutoff have the default value 10 1.
protocols.docking.DockingProtocol: Scoretype: interchain_contact score: -12.5, cutoff: 9.99
protocols.docking.DockingProtocol: Scoretype: interchain_vdw score: 1.30527, cutoff: 1

Post Situation: 

Rescoring protein docking decoys to get Irms

Category: 
Docking

Hi,

I'd like to rescore protein docking decoys to calculate the Irms (interface rms) against the lowest energy decoy. If I rescore using the scoring application, I can get the overall rms but not the Irms. I've tried including flags like -evaluation:Irms but can't seem to get it to work. Also, although less important, is there away to apply the same scoring as the docking application does - without specifying any scoring patches or weights or anything the overall score is completely different to the docking output score.

Cheers.

Post Situation: 

ERROR:: Exit from: src/core/fragment/ConstantLengthFragSet.cc line: 116

Category: 
Docking

Dear all,
when I run the ab_initio Flexpepdock protocol, I got this error :src/core/fragment/ConstantLengthFragSet.cc line: 116
Can someone give me some comments?
this is my flag:
-s eq_1_0001.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database

-out:file:silent decoys.silent
-out:file:silent_struct_type binary

-pep_refine
-lowres_abinitio
-rep_ramp_cycles 10

-ex1
-ex2aro
-use_input_sc
-constant_seed
-jran 12456

-frag3 ../NullFragments0/output_files/frags.200.3mers

Post Situation: 

residues_patch_selectors CENTROID_HA

Category: 
Docking

Hi Rosetta guys:)
Question about seemingly odd behaviour going from local rosetta run (rosetta_2014.16.56682_bundle) to mpi (2014.20.56383.mpi) and of course a slightly newer version of Rosetta3.5 though both are 3.5.

My normal docking scripts contains the flag
-residues:patch_selectors CENTROID_HA

this script runs smoothly.
When running on mpi I can do regular docking, but when introducing this flag (need it for SAXS runs), rosetta tells me that there is no such command on the top level.

Post Situation: 

Minimising space exploration during docking

Category: 
Docking

Hello,

I am trying to dock a single helix onto a specific region of a protein. When running a docking simulation using Pyrosetta the helix moves to another site on the protein. Is it possible to only allow the helix to explore a certain region of the target protein?

Many thanks in advance,

Alexander

Post Situation: 

Snugdock+ensembledock usage

Category: 
Docking

Hi all,

I have a quick question:
i have submitted 5 antibody sequences to Rosie and for each of them got ten lowest-energy structures. I have the solved structure of a protein X. I read the paper of Snugdock, got excited by the idea of using snugdock with ensembledock together and now want to perform a docking of my protein X using the models i got from Rosie.

Post Situation: 

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