Lots of Prepacking Jobs for Snugdock Failing
Submitted by katherinemccoy on Tue, 2023-02-28 18:17
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Docking
how to control alignment for energy_based_clustering
Submitted by xfradera on Tue, 2023-02-28 10:13
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
Submitted by yang on Thu, 2023-02-16 04:37
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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How to change the axes of "-spin" in docking_protocol
Submitted by Zehui Zhou on Mon, 2023-02-13 22:06
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St13runtime_error in Rosetta ligand docking
Submitted by syntekabio2019 on Thu, 2023-02-09 18:18
Category:
Docking
Hi all
I'm trying to dock the ligand into receptor with rosetta ligand docking with following command line
mpirun -np 20 rosetta_scripts.mpi.linuxgccrelease @options
where options file looks like this
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Run protein-protein docking parallelly by mpi
Submitted by Zehui Zhou on Thu, 2023-02-02 06:23
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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Should all input structures to energy_based_clustering have an output pdb file?
Submitted by Brian Wiley on Mon, 2023-01-30 20:42
prepack - residue count fails
Submitted by xfradera on Fri, 2023-01-27 06:36
Category:
Docking
Hi, I'm trying to prepack a complex for ensemble docking with this command:
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Snugdock Error: The sequence position requested was greater than the number of residues
Submitted by stannowitz on Tue, 2023-01-17 07:37
snugdock(sequence position requested was greater than the number of residues in the pose)
Submitted by lei on Thu, 2023-01-12 01:40
Category:
Docking
Dear users,
When I did snugdock, my native input structure and snug input structure share the same number of residues and residue indexes, but the error still shows up "sequence position requested was greater than the number of residues in the pose".
I attach both files and appreciate any suggestion. Thanks!
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