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computing Pnear for Rosetta ligand docking

Submitted by rohi on Mon, 2021-02-01 08:27
Category: 
Docking

Hello,

I am calculating the Pnear for the Rosetta ligand docking outputs to evaluate the funnel-likeness of energy vs RMSD by treating the lowest energy model as the native structure. Is it right to use binding energy and ligand RMSD (no superposition) as E and RMSD in Pnear formula? I see in the papers it is used for de novo designs and they use the total energy and general RMSD.

I really appreciate your help.

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Rosetta 3 - General

Issues with angle Constraints during Docking

Submitted by LeonhardJS on Thu, 2021-01-28 04:40
Category: 
Constraints

Hello,

I am setting up Docking simulations of 2 Monomers of a protein that forms monolayers at interfaces (HFBI, pdb entry 2fz6 ), so I need to constrain the possible Docking configurations to stay within the x-y plane and only beeing allowed to slightly change its orientation, due to a exposed hydrophobic patch.
I tried to use a combination of 2 angular and one Dihedral constraints. The constraint file looks like:

AngConstraint.cst:
"

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Rosetta 3 - General

Help - Protein-Protein interface design

Submitted by Dinesh Kumar on Thu, 2021-01-28 00:47
Category: 
Design

Hello everyone!!

I am trying to work on the protein-protein interface design using rosetta scripts.  I am new to running rosetta scripts. So, I kindly need help on that. 

I ran the configure file given in the first step which threw me an error of Nobsub in path. I tried installing bsub and adding paths to the bash file but still wasn't able to proceed further. 

Kindly help me out if there are any mistakes or details i may have missed in setting up the run.

Thanks in advance

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Rosetta 3 - General

Modelling humanized camelid like antibody

Submitted by terabithia2011 on Tue, 2021-01-26 10:12
Category: 
Structure prediction

Dear Rosetta community,

I went over the antibody structure prediction tutorials and now in the process of modeling structures for my custom sequence which has 27 aa's in the CDRH3. When I ran the following command,

antibody.linuxgccrelease -fasta cfab.fasta

I got the following error 

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Rosetta 3 - Applications

Creating fragment files for proteins less than 27 aa in length

Submitted by Poladu on Tue, 2021-01-26 07:50
Category: 
Fragment Generation

Good day.
I'd like to make abinitio structure prediction using rosetta of some small proteins (e.g. 2jof, which length is 20 amino acids). 
Such prediction requires fragment files, which can be generated using web Robetta Server or by youself using PSI-BLAST.
However, when i tried to submit a job on Robetta there was an error:
Sequence length must be between 27 and 1000 residues
Similar restriction was described in rosetta manual dedicated fragment-files:

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Rosetta 3 - Applications

Question with rosetta AbPredict tutorial

Submitted by terabithia2011 on Mon, 2021-01-25 09:24
Category: 
Structure prediction

Hi,

I am new to rosetta and just started working on some tutorials. I am currently trying to use AbPredict code to generate sample structures by trying to execute tutorial documents at https://zhuanlan.zhihu.com/p/82235565 and also at rosetta_bin_linux_2020.50.61505_bundle/main/demos/tutorials/AbPredict. However, I am having following questions. 

1. create_run.sh file at the rosetta_bin_linux_2020.50.61505_bundle has a syntax issue and the one with the link works perfectly.

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Rosetta 3 - Applications

antibody.linuxgccrelease- output models don't have the same sequence as the input fasta

Submitted by agctomer on Thu, 2021-01-21 15:35
Category: 
Structure prediction

hi,

I am using antibody.linuxgccrelease aplication in order to model camiled heavy chain only antibodies.

when using the command: 

antibody.linuxgccrelease -exclude_homologs true -vhh_only -fasta my_fasta.fa | tee grafting.log

 

for example with my_fasta.fa:

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