Alternatives to DockMCMProtocol
Submitted by swirt on Thu, 2021-01-28 17:37
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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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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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clustering ligand binding mood by ligand RMSD
Submitted by rohi on Tue, 2021-01-26 21:11
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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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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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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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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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ValueError: can only read V2000 format files
Submitted by egecav on Wed, 2021-01-20 13:49
Category:
PyRosetta
I'm providing the molfile_to_params.py with the enzyme-ligand complex of my molecule but unfortunetly it gives the "ValueError: can only read V2000 format files" error. Previously i gave it the individual ligand file and it processed with no problems. But when i try to process this file it doesn't seem to work. I suspect the problem is about the chemical table file formats and something in my code is from V3000 but i'm a begginer so i don't know what.
I will attach the text files of both the ligand .mol file and the complex .mol file.
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CoupledMoves not altering backbone coordinates?
Submitted by amorin on Wed, 2021-01-20 11:38
Category:
Design
HI All,
I'm beginning to play around with CoupledMoves for flexible backbone design and I am unable to get it to alter the protein backbone coniguration.
When I run the tutorial here (https://github.com/Kortemme-Lab/coupled_moves-tutorial) it works. But when I try and apply that (or similar) command to another protein it will deisgn the sequence, but all the output pdbs have no coordinate changes.
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