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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.
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?
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:
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.
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:
I'm quite new to Rosetta (and computational approaches in general, I've only been using linux and bash-based interfaces for about 6 months) and I've spent a few weeks trying to understand the docking process, which I think I understand fairly well. I've run into a problem that I hope you can help me with. Apologies for any naivety/confusion/incorrect terms that I use, I'm still very much an amateur so I might not explain myself in the best way.
What I want to do
I am new to Rosetta3 and jsut trying to dock some generated ligands into a protein PDB. Based on the generated structures it appears the docking program is working well however, when I look at the score.sc file the rms vlaues for all the generated structures is nan. I do not really understand if I should be expecting rms values. I am docking a ligand into an unbound protein substrate. Any information would be helpful.