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Docking

error in ligand docking

Category: 
Docking

 

Hello

I am doing ligand docking and get an error below, Could you tell me why chain 1 is not directly built by any jump and how I can fix it? Thanks

File: src/core/pose/chains_util.cc:506

[ ERROR ] UtilityExitException

ERROR: Chain '1' is not directly built by any jump.

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How to add additional rounds of design and optimization in Rosetta scripts?

Category: 
Docking

Hello,

I am using RosettaLigand design protocol to design protein binders for a small molecule. The tutorial I referred to is Mr. Rocco Moretti's paper ( Methods Mol Biol. 2016 ; 1414: 47–62. doi:10.1007/978-1-4939-3569-7_4.).

According to the tutorial, "the provided protocol only does one round of design and minimization. Additional rounds may be desired for further refinement. Simply replicate the low_res_dock, design_interface, and high_res_dock lines in the PROTOCOLS section to add additional rounds of design and optimization."

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High Resolution Docking with DockMCMProtocol

Category: 
Docking

Hello, I am working on protein-protein docking with a fairly refined (fastrelaxed) experimental complex.

As such, high resolution docking seems to be the way to go, but I'm a little bit confused with which class to use in pyrosetta.rosetta.protocols.docking :

- Can't get DockingHighRes() to work (RuntimeError: Tried to call pure virtual function "DockingHighRes::apply")

- Pyrosetta Notebooks hint at DockMCMProtocol, but I'm not sure whether this should be used alone, or in conjuction with 

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ERROR: Unable to fill in missing atoms.

Category: 
Docking

Could you please help with the following issue (I am using rosetta3.12/rosetta_bin_linux_2020.08.61146_bundle):

core.conformation.Residue: [ ERROR ] Cannot build coordinates for residue TGT at position 111: missing too many atoms. core.conformation.Residue: [ ERROR ] Missing atoms are: C11 N1 C20 C9 C10 C17 N3 N2 C13 C2 N4 C19 S1 C14 C3 C15 C4 C18 C16 C7 C5 C12 C1 C6 C8 H1 H9 H16 H17 H18 H19 H20 H6 H7 H8 H10 H11 H12 H13 H14 H15 H4 H2 H3 H5

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I need some help for using pHDock applications(histidine protonation / pH-dependent binding)

Category: 
Docking

Hi everyone

I'm beginner of ROSETTA/Linux commandline, so please explain problems easily

I can model protonated histidine residue(HIS_P?) by docking_prepack application

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FlexPepDocking

Category: 
Docking

Hello,

I have recieved this warning when trying to use FlexPepDocking refinement protocol for a tyrosine phosphorylated peptide.

core.util.switchresiduetypeset: (0) [ WARNING ] When switching to centroid mode, a normal replacement type for residue TYR:phosphorylated can't be found.

core.util.switchresiduetypeset: (0) [ WARNING ]     an autogenerated replacement type is being used instead.

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Extracting top score PIPER models

Category: 
Docking

Hello,

I am docking a peptide in a receptor with PIPER using the steps in https://www.rosettacommons.org/docs/latest/application_documentation/docking/flex-pep-dock.

The step 2.III of the PIPER-FlexPepDock protocol uses the apply_ftresult.py script which is not present in the source. Where can I get this script or an equivalent?

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