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Error arises when installing rosetta_src_2021.16.61629_bundle with scon

Submitted by Sunyp_IM on Tue, 2021-09-28 08:08
Category: 
Compilation

Dear all,

   I am trying to install rosetta_src_2021.16.61629_bundle in CentOS system (Python 3.8.8) using:

         ./scons.py -j8 mode=release bin

   However, it produces the following error:

         AssertionError: Parameters of BuildFlags must be lists
         scons: done reading SConscript files.
         scons: Building targets ...
         scons: `bin' is up to date.
         scons: done building targets.

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Rosetta 3 - Build/Install

antibody - sequence position requested was 0

Submitted by jremmel on Mon, 2021-09-27 12:26
Category: 
Structure prediction

Hi,

I am trying to do some antibody structure prediction. During the grafting step for the sequence I am working with, it seems to get through making 4 models, but then crashes with the error message: 

[FILE]: src/core/conformation/Conformation.hh

[LINE]: 509

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

Anyone have any idea what is going wrong here? 

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Rosetta 3 - Applications

Error reading in/out glycosylated silent file - "Can't create a polymer bond after residue due to incompatible type"

Submitted by amorin on Mon, 2021-09-27 12:16
Category: 
Chemically Modified Residues

Hi all,

I'm having trouble extracting (or reading in) a previously rosetta glycoslylated structure from a silent file after relaxing it. Attempting to either extract or read back in the relaxed structure from a silent file results in the following error:

 

Can't create a polymer bond after residue 506 due to incompatible type: ->4)-alpha-D-Glcp:non-reducing_end

 

The protocol I used is as followes:

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Rosetta 3 - Applications

Enzyme design gets 0 hit

Submitted by cryosky on Sun, 2021-09-26 13:24
Category: 
Enzyme Design

Hi,

I'm doing a de novo design of an enzyme to fit in a new molecule. There is a protein structure papers that proposed the interactions between another molecule and residues in the protein and I found two molecules share the same atoms in these interactions. So I transfer these interactions and written them into the cst file. There are a total of 3 blocks. However, I found the program reports 2000+ hits after the first round but 0 hits after the second round. What's causing this error and what should I do to get more hits?

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Rosetta 3 - General

Symmetry breaks due to small structure gaps

Submitted by dbiedermann on Mon, 2021-09-20 17:39
Category: 
Symmetry

Hi everyone,

I'm having trouble re-designing a 2-component symmetric nanoparticle with small gaps along lines that connect symmetry axes. The starting pdb looked good, so I selected 2 chains that define the unit cell and apply a symmetry file to enable the computational savings associated with symmetry. However, the symmetric docking step that's triggered by the rosetta.protocols.symmetry.SetupForSymmetryMover method seems to smush the chains together, resulting in a smaller radius nanoparticle with VdW clashes.

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PyRosetta - General

Python2 script in Rosetta3.13

Submitted by ddhoyo on Wed, 2021-09-15 04:05
Category: 
Docking
Good morning,

    I am trying to use Rosetta (v3.13) for  drug screening analysis and I 
    found a specific script in the Rosetta3.13 package (also in other 
    versions) which has some python2 code that hampers its use in the 
    current python3.

    The script is: 
    rosetta_bin_linux_2021.16.61629_bundle/main/source/scripts/python/public/batch_molfile_to_params.py

    Python2 code:

    1) Lines 110, 114, 117: print without brackets

    2) Lines 40, 116: "is not" instead of "!="
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Rosetta 3 - Applications

pmut and scoring

Submitted by ldlamini on Tue, 2021-09-14 00:46
Category: 
Design

Hello all,

I am doing semi-rational design of my protein. So far I have one mutation that increases thermostability identified in vitro. However, Rosetta didn't predict this mutation in pmut scan. When I scored the protein variant with this mutation, the score was better than all the mutations predicted by Rosetta.

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Rosetta 3 - General

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