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Docking

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...

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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( ... ).

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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.

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Evaluate Docking Result

Category: 
Docking

Hi,
I have a set of outputs conformation from rosetta after hotspot placement. It's a docking of antigen and antibody. So, how should i evaluate the results? I filtered out the top100 lowest ddG, but, when proceeding to SASA, shape complementarity score and number of hydrogen bond, the results varied. Some having more H-bond with lower Sc score ( around 0.3-0.4). Some with no H-bond but better Sc score.

For example:
A: -31 ddG, 3 H-bond, 2641 SASA, 0.565 Sc
B: -29 ddG, 0 H-bond, 2050 SASA, 0.610 Sc
C: -20 ddG, 5 H-bond, 2039 SASA, 0.323 Sc

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Failure in local docking

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

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