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Docking

How do you combine two .pdb protein structure files of the same protein?

Submitted by nasim.soltani58 on Sun, 2020-11-22 23:14
Category: 
Docking

I have a *.pdb file of one protein. I need to do protein protein docking for this protein (I have the original one and I will also make a duplicate of it). What is the best way to combine the original one and the duplicated in one pdb file (I'm doing this to prepare the final pdb for docking).

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PyRosetta - General

how do i unding properly?

Submitted by patcD on Fri, 2020-11-20 00:38
Category: 
Docking

Hello guys,

 

i am new to pyrosetta and I am having some issues with making sure I am undocking properly. 

I have a pdb file with a receptor with a receptor, 2 metal ions, a cofactor and then a substrate. It is arranged in a pdb file, with the receptor + metals beeing chain A, cofactor B, ligand X.

 

how do i unbind only the X chain properly? The tutorial is set up for a different problem, and i am struggling to valdidate the results. It also said that you could use 

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PyRosetta - General

Prevention of the negatively charged Nitrogen protonation by coupled_moves

Submitted by Corvin on Wed, 2020-11-18 02:56
Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear sir and madam,

I have met with the unfavourable addition of 2 Hydrogen atoms onto sulfonamide Nitrogen instead one (NH2 instead of NH) on a ligand during the coupled_moves docking application runs. It is perfomed by the following command:

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Rosetta 3 - Applications

error in ligand docking

Submitted by rohi on Fri, 2020-11-13 10:52
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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Rosetta 3 - General

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

Submitted by Nicole Deng on Tue, 2020-11-03 19:05
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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Rosetta 3 - Applications

High Resolution Docking with DockMCMProtocol

Submitted by hjacomet on Thu, 2020-10-29 09:02
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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PyRosetta - Applications

ERROR: Unable to fill in missing atoms.

Submitted by mieczyslaw on Tue, 2020-10-20 09:43
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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