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Error using pHDock

Submitted by SenyorDrew on Thu, 2016-08-11 05:56
Category: 
Docking

Hi,

I'm having trouble running pHDock (in an attempt to model protonated histidines).  I'm using the command-line arguments described in the pHDock paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263365/):

~/rosetta/bin/docking_prepack_protocol.linuxgccrelease -s input_prep_sc.pdb -partners AB_C -dock_ppk -pH:pH_mode -pH:value_pH 5.6 -score:weights packing.wts -ex1 -ex2aro -unboundrot input_prep_sc.pdb

Fails with the error:

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Rosetta 3 - General

Collecting all decoys from batch files

Submitted by aep on Sun, 2016-08-07 12:23
Category: 
Structure prediction

Greetings.

For anyone who's used the RASREC-based protocols in Rosetta, I'm wondering if you know of any script or straightforward way to collect the decoys generated across all batch files. I'd like to be able to plot all decoys on an energy-rms plot. I know Rosetta reuses decoy tags, so I'm not sure how to go about it. I've looked into the cluster application, but I'd like to use the centroid and/or full-atom scores for direct manual plotting as well.

Any advice would be much appreciated.

Cheers.

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Rosetta 3 - Applications

[Mover] is not known to the MoverFactory

Submitted by Jhreed on Fri, 2016-08-05 12:23
Category: 
Design

Hi,

I'm running the 2016.20 weekly release of Rosetta and am running into some issues.

The bottom line is that this error comes up when I attempt to use certain Movers:

Error: ERROR: Exception caught by rosetta_scripts application:FastDesign is not known to the MoverFactory. Was it registered via a MoverRegistrator in one of the init.cc files (devel/init.cc or protocols/init.cc)?
Error:

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Rosetta 3 - General

Docking-Error 500

Submitted by edebenedictis on Wed, 2016-08-03 12:34
Category: 
Docking

Dear all,

I submitted a protein-protein docking job (24902) and kept track of it through the queue.  I recently was emailed when it completed, but anytime I try to access the job page, I see the message: "Error 500 We're sorry but we weren't able to process this request."  This is both accessing from the link in my email, and from the ROSIE queue.

Please let me know if there is anything I can do to resolve this, or if I should just resubmit the job.

Thank you,

Elizabeth

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ROSIE - General

Enzyme Design with additional covalent backbone bonds

Submitted by mwfranklin on Wed, 2016-08-03 10:23
Category: 
Design
Enzyme Design
Constraints
Non-Canonical Peptides

Hey everyone,

I am trying to design a protein with a covalent bond between the C of Thr and the N of Gly with a Tyr in between them (imitating the chromophore from GFP for perspective). Because of this odd 5-membered ring formation, I used Thr/Gly with a generous distance constraint between them in my CST file when I ran RosettaMatch to find likely sites in my scaffold proteins. My sites place the two backbone atoms ~4-5A apart.

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Rosetta 3 - Applications

antibody.py

Submitted by franfdez on Mon, 2016-08-01 08:12
Category: 
Loop Modeling
PyRosetta

Dear all,

I am using the antibody.py script that comes with PyRosetta (rosetta_src_2016.13.58602_bundle, v3.6) and associated software to generate structural models for VH/VL sequences. For most of the sequences that I am using as input, the script terminates at the antibody_graft step with an error (pasted below):

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PyRosetta - Applications

Convert Rotamer Vector to Chi Angles

Submitted by L-Allanine on Sat, 2016-07-30 09:16
Category: 
Enzyme Design

Dear PyRosetta Community,

I am attempting to find the closest rotamer to each residue in a protein and then obtain the chi angles for each of those closest rotamers. I have successfully used the core.pack.dunbrack.rotamer_from_chi function to obtain the rotamer vector, thanks to the topic "Rotamer information from pose." Is there a reverse function, essentially "chi_from_rotamer," that will return the chi angles that correspond to the rotamer vector that rotamer_from_chi yields?

Thank you.

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PyRosetta - General

how build (N-terminal 17 residues) structre /fragment file generation

Submitted by venkatazb on Wed, 2016-07-27 23:56
Category: 
Structure prediction

Greetings, 

1) How to generate the n-terminal region say 17 residues (loop only, no homologs structure available in pblast )

2) Entire protein sequence structure got Robetta n-Terminal is only loop in MD run it’s not converging. 

Accordingly plan to do loop model is that way good way? or any other Rosetta application will help in is this situations

Kindly let me know  

Awaiting your replay

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Rosetta 3 - General

error--rosetta fragment‐based refinement protocol for refinement against EM density

Submitted by gsuchunli on Mon, 2016-07-25 13:35
Category: 
Scoring

I am trying to fit my pdb structure into EM density and the following information happened:

tupdens=======================

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================

protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MinMover - cenmin=======================

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