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Docking

nbr_atom in ligand docking

Category: 
Docking

Dear all,
I run ligand docking protocol to dock a small chemical on my protein.
I set up the inital position of ligand is "-start_from 1.36 50.07 23.4".
Follow the document, the nbr_atom of the ligand is chosen near the inital position of ligand. But when I check the log file, I saw the nbr_atom of the ligand is far away from the inital position of ligand: 44.03500058226830 112.4592971897935 22.25074880071337
4.886590717968414 0.06526207982382815 17.92231676318689

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the output of ligand docking

Category: 
Docking

Dear all,
I run the ligand docking protocol to dock a small chemical to protein.
this is my flag
-packing
-no_optH
-ex1
-ex1aro
-ex2
-docking
-dock_pert 30 5
-ligand
-improve_orientation 1000
-minimize_ligand
-harmonic_torsions 10
-minimize_backbone
-harmonic_Calphas 0.3
-soft_rep
-old_estat
-start_from 1.36 50.07 23.4
-protocol abbrev2

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RosettaProtein_Docking

Category: 
Docking

Hi Everyone, I was wondering if anyone knows how to set path for saving output pdb files in Rosetta protein docking. I was using following command line to run protein docking, didn't found any saved output pdb files.

/path to/rosetta_2014.35.57232_bundle/main/source/bin/rosetta_scripts.default.linuxgccdebug @docking.options -parser:protocol docking_full.xml -database /path to/database/ -out:suffix _full -nstruct 50 > docking_full.log -restore_pre_talaris_2013_behavior

Docking.option file

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docking with constraints and flexible bb

Category: 
Docking
Loop Modeling
Constraints

Hi,
I am doing unbound docking and i believe I have enough biological info to locate the binding interface and rough orientation. Doing the docking manually (or with the low res protocol) suggests that there's some conformational change in the interface that I would like to model. I'm guessing this is not something that I can accomplish with the old docking_protocol commandline app. I did see a flexible_bb_docking option but that appears to be undocumented? Maybe I can do this via the ensembles options?

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Prepack step fail in docking2

Category: 
Docking

I am trying to dock the variable domains of an antibody with its protein target in docking 2. The structure of the variable antibody domains are predicted from homology. I have a few different antibody and for all except one this works fine. One however gives the error message Prepack step failed. Check your input files. I have repredicted the structure of the antibody with various programs, but it keep on failing. What can the problem be? Is there any online program (in Rosie for instance) where I can check my input before I try to dock?

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Resfile as a input for InterfaceAnalyzer

Category: 
Docking

So, I have a pdb complex of a virus and antibody and I wanted to compute the binding energy of the given complex. I know that I need to use InterfaceAnalyzer for this task, but the problem is that the input of the InterfaceAnalyzer application is a resfile. So, how am I supposed to connect these two, the resfile and the pdb file ?

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How to prepare the pdblist file for docking_ensmble in Rosetta3.4

Category: 
Docking

Did anyone do ensemble docking using rosetta3.4?
I don't know how to prepare those seemed like energy score(lowres_reference_energies_ , and highres_reference_energies_ from source code) at
the end of pdblist file?

An example of the pdblist is below:

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rotamer library in coupled_moves

Category: 
Docking
Enzyme Design
Small Molecules

Hello, 

 

Recently, I had a chance to see a presentation about coupled_moves. There is hardly any information about it since the paper isn't published yet but I figured I would give it a try anyway. What I want to do is to redesign enzyme specificity for a new substrate . The problem is including rotamers library of my new substrate. 

 

I created ligand rotamers with Frog2 (no acces to MOE or OpenEye) and created params files with:

 

"molfile_2_params.py rotamers.mol2 --conformers-in-one-file".

 

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How to use Rosetta to DISCARD a protein-protein docking interface?

Category: 
Docking

Suppose I have two proteins A and B. I know they bind but I don't know the conformation of the complex. There is a region of interest in the surface of protein A, and I have reasons to believe that A and B DO NOT bind through this region. How can I use Rosetta to DISCARD a docking interface?

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