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Docking

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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how to control alignment for energy_based_clustering

Category: 
Docking

Hi,

I am using the energy_based_clustering application to cluster results from a protein-protein global docking job. One of the partners is kept fixed, so I would like to cluster based on the RMSD of the moving partner alone, without any alignment. I assume that the clustering algorithm is aligning the whole structure to minimize RMSD. Is this correct? If it is, is there a way to skip the alignment and calculate the RMSD directly from the input structures?

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ligand_docking

Category: 
Docking

Hi , I'm beginner to Rosetta . In ligand_docking , it is said "chain_id F does not exist" . There are two ligands and one receport to dock ,   I can not define chain F or chain X (in my dock.xml).  I can not undersstand  some answers about this question. I wish receive the answer.

 

the process in ligand_docking:

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Run protein-protein docking parallelly by mpi

Category: 
Docking

I run docking_protocol parallelly by mpi (Command: mpiexec -np 10 $ROSETTA_BIN/docking_protocol.mpi.linuxclangrelease @flag_docking).

But the error below occurred.

[ERROR]

-----------------------------------------------------------------------------

Primary job terminated normally, but 1 process returned.

a non-zero exit code. Per user-direction, the job has been aborted.

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