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Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi

Submitted by SamuelGong on Fri, 2023-01-27 06:20
Category: 
Scoring

Hi,

using a flag containing options "-dunbrack_prob_buried_semi 0.8" and "-dunbrack_prob_nonburied_semi 0.8", errors appear like:
...................................
File: /home/shanghai/RationalDesign/Rosetta3.9/rosetta_src_2018.09.60072_bundle/main/source/src/utility/options/OptionCollection.cc:1314
Option matching -dunbrack_prob_buried_semi not found in command line top-level context

...................................

 

the flags and log file were attached.

Please help, thanks

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Rosetta 3 - General

Grafting using antibody.mpi.linuxgccrelease , the modelled structure does not have constant region of the antibody.

Submitted by SubhaK on Thu, 2023-01-26 21:29
Category: 
Structure prediction

Hello all,
Using this command to graft from a specific template
antibody.mpi.linuxgccrelease -antibody:blastp /home/rosetta/ncbi-blast-2.13.0+/bin/blastp -fasta antibody.fasta -antibody:h1_template  pdb_id
The modelled structure does not have constant portion of the antibody.

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Rosetta 3 - General

Access to GitHub Denied

Submitted by Lucia_G on Wed, 2023-01-25 07:13
Category: 
ROSIE

Hi,

I am contacting you as I cannot login in GitHub portal with my ROSIE account credentials to perform docking analysis. 

My credentials are:

Lucia93

University of Warwick

I also created an account on Rosetta Commons website, but neither those ones are accepted for the login.

Can someone help me with this please?

Best wishes,

Lucia

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Unsolved
Forums: 
ROSIE - General

farfar2 failed

Submitted by Kamonwan on Mon, 2023-01-23 18:41
Category: 
Structure prediction

Hello

I am trying to model a modified 3D RNA structure using farfar2. 

Job 「№108206」has failed with the message: No output silent files were produced in the FARFAR2 step; please double-check your inputs!

I have checked the input sequence and dot bracket files (PDB file exceeds the maximum allowed size for upload). I don't know, how to solve it. Attaching the input flies. Could someone please help me sort the error.

Thank you

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Forums: 
ROSIE - General

Grafting using antibody.mpi.linuxgccrelease and specifying custom template which doesnt have pdb id.

Submitted by SubhaK on Wed, 2023-01-18 23:33
Category: 
Structure prediction

Hello all,
Using this command to graft from a specific template
antibody.mpi.linuxgccrelease -antibody:blastp /home/rosetta/ncbi-blast-2.13.0+/bin/blastp -fasta antibody.fasta -antibody:h1_template  pdb_id

Can we use the same approach for grafting where we dont have a pdb id to specify template and use a specific structure instead ??
 

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Rosetta 3 - Applications

snugdock(sequence position requested was greater than the number of residues in the pose)

Submitted by lei on Thu, 2023-01-12 01:40
Category: 
Docking

Dear users, 

When I did snugdock, my native input structure and snug input structure share the same number of residues and residue indexes, but the error still shows up "sequence position requested was greater than the number of residues in the pose".
I attach both files and appreciate any suggestion. Thanks!

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Forums: 
Rosetta 3 - Applications

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