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Docking

Prepack step fail in docking2

Submitted by gretahultqvist on Thu, 2015-06-11 00:20
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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ROSIE - General

Resfile as a input for InterfaceAnalyzer

Submitted by palak8669 on Sun, 2015-06-07 21:46
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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Rosetta 3 - Applications

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

Submitted by sunlufinal on Mon, 2015-06-01 19:27
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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Rosetta 3 - General

rotamer library in coupled_moves

Submitted by mtyras on Fri, 2015-05-29 07:46
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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Rosetta 3 - Applications

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

Submitted by cossio on Tue, 2015-05-26 06:24
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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Rosetta 3 - Applications

Ensemble Docking in Rosetta3.5?

Submitted by protos_heis on Fri, 2015-05-22 06:42
Category: 
Docking

I apologize if this has been asked before, but I couldn't seem to find any information on it. Is the EnsembleDock protocol available in Rosetta3.5? I don't see a specific executable for it in the rosetta/source/bin directory. Do I just use -l <pdblist> instead of -s <pdbfile> in the normal docking protocol? And can I still use constraints in EnsembleDock?

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Rosetta 3 - Applications

SymDock with constraints

Submitted by felipet on Thu, 2015-05-14 09:01
Category: 
Docking
Constraints
Symmetry

Dear all

I been trying to perform a symmetric docking with constraints and it is not working. Reading old post residue number must be carefully set. For some reason the low-res filter is dumping all the solutions ("STRUCTURE FAILED LOW-RES FILTER"). I imagine that has to be with how I define the constraints but I even tried using AtomPair CA 52 CA 182 GAUSSIANFUNC 50.0 50.0. Please can someone have a hint of what is going on?

thanks in advance

felipet

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Rosetta 3 - Applications

Minimization Issue: Coarse Graining to All atom modeling

Submitted by abolia on Tue, 2015-04-28 10:52
Category: 
Docking
Design
Loop Modeling

Hi all,
I want to get an all atom model of my coarse grained protein structure (after adding all the side chains back). I have been using the repacking algorithm to do so, but unfortunately its not doing the job. The side chains are not packed properly. Can you help me suggesting on how to go from coarse grained protein to get an all atom model for my protein. Is there any minimization protocol that can take care of this. Kindly let me know.

Thank you.

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Rosetta 3 - General

Rosetta dock irmsd

Submitted by Pernille on Sun, 2015-04-26 13:51
Category: 
Docking

Hi Rosetta people

I have an odd problem concerning the interface rmsd output from rosetta dock.
I have two structure outputs from different runs. Only difference is using saxs as restrain in one run otherwise the scripts are identical.
I get better irmsd from the saxs run (0.333 vs. 1.116) but when looking at the structures there is barely any difference, I have checked rotamers as well.

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Rosetta 3 - Applications

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