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Docking

Intel MPI: early exit due to job process stopped.

Category: 
Docking

Hello, I am using rosetta docking_protocol compiled with Intel MPI (from Intel® oneAPI Toolkits 2020), and I have some problems / bug reports.

I requested 3 output poses with '-nstruct 3' and I ran 'mpirun -n 3 docking_protocol.mpi.linuxiccrelease ...' to start one master rank and two slave ranks. However, when one slave (rank 2) finished its jobs and master will send spin down signal:

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Docking one protein into interface between two other proteins

Category: 
Docking

Hello world, 

How can I dock one protein into interface between two proteins? I am new to rosetta software and I am still leraning. I study a protein that bridges two other proteins togeter and I was wondering how can I model that? I would apreciate your input in directing me to the tutorials or documentation. 

Thanks. Cheems

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Missing atoms, unable to fill in missing atoms

Category: 
Docking

Hello Rosetta people,

I performed a protein protein docking of a protain A + ligand A (74 atoms) noted as binary_complex to protein B, and got warning of missing atoms, still could get docked P-P poses, however, the ligand is not intact, some atoms missed in the output binary_complex. I also added the -ignore_unrecognized_res flag in the command.

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Missing atoms, unable to fill in missing atoms

Category: 
Docking

Hello Rosetta people,

I performed a protein protein docking of a protain A + ligand A (74 atoms) noted as binary_complex to protein B, and got warning of missing atoms, still could get docked P-P poses, however, the ligand is not intact, some atoms missed in the output binary_complex. I also added the -ignore_unrecognized_res flag in the command.

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How many rifdock can I run at a time on a 64 CPUs and 512GB memory server?

Category: 
Docking

How many rifdock can I run at a time on a 64 CPUs and 512GB memory server?

I tried 8 rif_dock_test running at a time, but I lost connection with my server several hours later(maybe 5 or 6 hours). My guess is the server was overloaded, so that the connection was lost. 

I used uptime command to check out, the system load is nearly 800%, does that mean I can only run one rif_dock at a time?

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question about antibody modeling and snugdock process option

Category: 
Docking

I am currently working on a simple test with antibodies.

I have a question in this regard, can I use deepab instead of rosetta antibody to create antibody structures? When I looked at the snugdock paper, it seems that there is an additional protocol when using a tool other than rosetta antibody, but I know that deepab creates structures based on rosetta. So I am wondering if I can proceed in the same way as rosetta antibody when using deepab. 

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XML validation failing

Category: 
Docking

I am trying to validate a .xml script to be used by rosetta_script application. I copied the .xml file from the paper:  Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein−Ligand Docking. But the valdation fails...

When I run,

validate_rosetta_script.default.linuxgccrelease -parser:protocol crystdock.xml -parser:script_vars sg=input random=0

 

Here is my XML:

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Extracting starting coordinates from ligand docking output

Category: 
Docking

I've done some ligand docking using cognate ligands, so used the starting coordinates of the input sdf file.  I now want to dock some analogues and want to use the same starting coordinates.  Is there a way to find what coordinates were used for the initial docking?

Thanks

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