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Docking

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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Strong bias in sampling observed in RosettaDock

Category: 
Docking

Dear Rosetta Community,

I am interested in flexible blind/global docking of a monomer to generate homo-dimers. For this I have used the RosettaDock application with -ensemble1 and -ensemble2 flags after passing the prepacked structure to -in file:s. I observe a strong bias in the output population of the docked dimers depending on what I pass in -in file:s. The docking commands are as follows:

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what factors determine the lowest (best) LigInterfaceEnergy score?

Category: 
Docking
Scoring
Small Molecules

Hi everyone.

We are docking small molecule ligands into non-enzyme proteins to get an idea of ligand distribution/convergence within the binding pocket, using the LigInterfaceEnergy mover. While the results are promising, ligands with the lowest LigInterface energy are sometimes outliers within the ligand distribution. There is no native structure to compare to other than the input pose.

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Global Docking with carbohydrates

Category: 
Docking

Hi everyone,

        I have some problems about protein and protein docking. I want to dock a peptide into protein using global docking. But there are some carbohydrates in my protein. After docking, the site of the protein bonds with carbohydrate and the carbohydrates bond each other have some error. And the score of the results are very high.

Generally, they should automatically dehydrogenate after docking. Did I miss some commands or how can I solve this problem?

I attach the output's image and following is my flag:

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