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the output of ligand docking

Submitted by phanvy on Fri, 2015-07-03 01:27
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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Rosetta 3 - General

Rosetta demos error

Submitted by jlburkhead on Thu, 2015-07-02 17:23
Category: 
Compilation

Perhaps this is a simple error due to my minimal experience, but I appear to have a good install of Rosetta on a new machine (MacOS 10.10.3). I went to run the demos and keep getting the following error:

Encounter error while executing: bash /Users/jlburkhead/Desktop/Rosetta/demos/public.run/abinitio/command.sh
*** Test abinitio did not run! Check your --mode flag and paths. [2015-07-02 15:39:53.664224]
Finished abinitio in 0 seconds [~ 1 test (100%) started, 0 in queue, 0 running]

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Rosetta 3 - Build/Install

RosettaProtein_Docking

Submitted by khadkab@mcmaster.ca on Tue, 2015-06-30 11:28
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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Rosetta 3 - General

docking with constraints and flexible bb

Submitted by mintseris on Mon, 2015-06-22 09:07
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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Rosetta 3 - Applications

AtomPair and SPLINE

Submitted by attesor on Sat, 2015-06-20 11:42
Category: 
Constraints

based the function from SplineFunc.cc, it seems different number of columns are required when using AtomPair and SPLINE (see code below). But the documentation only says "replace <filename> with EPR_DISTANCE". This would definite leads to compaint of Rosetta. 

 void SplineFunc::read_data( std::istream &in)

{

 

utility::io::izstream potential_file;

 

// If constraints::epr_distance specified, read in histogram from database

if( basic::options::option[ basic::options::OptionKeys::constraints::epr_distance]() )

{

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Rosetta 3 - General

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

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