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"Angle constraint: 0-length bonds" error

Submitted by purvi24 on Sun, 2019-07-28 10:09
Category: 
Enzyme Design

Hi,

I am trying to design the binding site of a protein with certain ligands and there is a common error that I encounter with various ligands (not all). The error says "Angle constraint: 0-length bonds". I checked the input structure and there are no atom clashes. I am not sure what is causing this error. If anyone has an idea, it would be a great help.

Thank you !

Purvi

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Rosetta 3 - Applications

FARFAR2 structure prediction give a circular RNA

Submitted by jitz on Thu, 2019-07-25 04:58
Category: 
Structure prediction

i have suplied Farafar2 with an RNA sequences of length 47. the server returns a complete circular structure. i dont have a template and am just giving the fasta file. when i give the dot-bracket structure along with the fasta file, it returns an error too.  

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ROSIE - General

Incomplete Error message

Submitted by tlc55555 on Mon, 2019-07-22 14:47
Category: 
PyRosetta

So, I have a code that is supposed to design an enzyme with constraints taken into account. I started it once, looping through a folder of pdb files (that one is still running, takes a while to design 375 pdb files), then just changed which folder and pdb files it would work with. Unfortunately, I then got an error message that cuts off before actually giving the error:

RuntimeError: 

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PyRosetta - Scripts

RosettaMatch

Submitted by xingqing326 on Mon, 2019-07-22 13:14
Category: 
Enzyme Design

Hi,

I was trying to run rosetta match with Rosetta/main/source/bin/match.linuxgccrelease   

The match was done successfully with older version of rosetta, but didn't work with Rosetta 3.10. It aborted because of an error of "ERROR: Assertion 'build_sets_[ build_set_id ].restype().has( "1HA" ) failed. ERROR:: Exit from: src/protocols/match/upstream/ProteinUpstreamBuilder.cc line 1210". I was wondering if there's a way to fix this. Many thanks.

 

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Rosetta 3 - Applications

PyMOLMover object has no attribute 'link'

Submitted by nleroy on Mon, 2019-07-22 07:51
Category: 
PyRosetta

Hi Guys,

I am trying to set up the PyMOLMover object to view structure manipulations. We have PyRosetta set up on a compter cluster, and I was going to have it run scripts and send structure info to another PyMOL instance on a separate computer on the same network - however it errors out when trying to assign an IP address to the link.udp_ip attribute. The code is simple and pulled straight from the following documentation/tutorial: http://www.pyrosetta.org/pymol_mover-tutorial

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PyRosetta - General

RosettaDesign

Submitted by ac.research on Sun, 2019-07-21 01:20
Category: 
Design

Hello Everyone,

I have been trying to find a solution to RosettaDesign where it can reliably design proteins.

I have tried the following protocols: 

FIXBB with resfile   - faield
FIXBB                - faield
FLXBB with blueprint - failed
FLXBB                - failed
Remodel              - failed

In each protocol I choose the lowest scoring decoy from 100 generated decoys. I run an abinitio simulation (25,000 decoys) but I do not get a funnel shaped plot.

 

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Rosetta 3 - General

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