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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.

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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

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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: 

FlexPepDock Concatenation

Category: 
Docking

Hello,

Thanks in advance for all those who help out with this issue. Using the FlexPepDock application, I have generated multiple decoys.silent files (binary) during docking. Multiple decoys.silent files were generated as I used a small cluster of 20 processors where each processor generated its own decoys_X.silent file. Now that I have successfully performed these docks, I would like to concatenate all of the decoys.silent files into a single decoys.silent file for analysis. Is it possible to simply use the method below...

Post Situation: 

Docking on mpi.

Category: 
Docking

Hi guys

Our local cluster has recently ,finallly, helped me to get the mpi Rosetta version installed.
RosettaDock seems to be working though I get some error messages. None of which i observe on my local computer.
1st:
Created 6242 residue types
Number of residue types is greater than MAX_RESIDUE_TYPES. Rerun with -override_rsd_type_limit. Or if you have introduced a bunch of patches, consider declaring only the ones you want to use at the top of your app (with the options) with the command option[ chemical::include_patches ].push_back( ... ).

Post Situation: 

Argument error when running D120_Ligand_interface.py

Category: 
Docking
PyRosetta

Hi,

I am trying to run D120_Ligand_interface.py sample script with the provided test_lig.pdb and ATP.params. I have placed the ATP.params file into (in PyRosetta main directory) /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types and added the path of the ATP.params file to the file /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt. When I run the script (in ipython - run D120_Ligand_interface.py) I get the following error message.

Post Situation: 

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