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Ligand docking error Could not find essential file trigger-00001.ligand_docking_protocol

Submitted by iphan on Mon, 2016-09-12 10:58
Category: 
ROSIE

Hello,

My attempts at ligand docking on Rosie (e.g. job 26146)  keep failing after less than 15min. I am getting no input error. The json logs return the error: 

  "log": "\nCould not find essential file trigger-00001.ligand_docking_protocol/score.sf in DB!\n",


I used Frog2 to generate my ligand sdf file and Chimera to estimate the starting x,y,z coordinates.

Any hints at what I might be doing wrong?

 

thanks,

Isabelle

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Unsolved
Forums: 
ROSIE - General

why is talaris2014 scoring fuction not used with ligand docking?

Submitted by banshee on Fri, 2016-09-09 01:19
Category: 
Docking

hi

someone who uses rosetta ligand docking protocol was asking why score12 was used for ligand docking and not the most recent scoring function which i believe is talaris2014? is it just because it has not been tested yet? or for some other reason? thanks.

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Unsolved
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Rosetta 3 - Applications

restrain multiple portions of proteins with MinMover

Submitted by Karol on Wed, 2016-09-07 08:29
Category: 
Design

Hi,

I want to restrain certain portions of my protein when doing cryo-EM modeling.

I was trying to modify the MinMover section of my XML file from

<MinMover name=cenmin scorefxn=cen type=lbfgs_armijo_nonmonotone
        max_iter=value tolerance=value bb=1 chi=1 jump=ALL/>
 to:

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Unsolved
Forums: 
Rosetta 3 - General

dock & design

Submitted by sdh_h on Fri, 2016-09-02 03:07
Category: 
Docking
Design
Constraints
Symmetry

Dear All,

I would like to simultaneously dock and design two (or more) identical subunits into a a symmetric homooligomer.

Input:

- backbone structure of a monomer (no sidechains!);
- initial arrangement of the subunits;
- constraints that precisely define interactions between the subunits.

Simulation:

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Unsolved
Forums: 
Rosetta 3 - General

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