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:
You are here
The problem hasn't been solved
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.
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:
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.
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.
I am trying to use RosettaAntibody in order to model a camiled heavy chain only antibody (pdb code: 1YC7_1).
when using the following command:
antibody.linuxgccrelease -exclude_homologs true -vhh_only -fasta 1YC7_1.fa | tee grafting.log
(I am using exclude_homologs in order to test its preformance, because this antibody structure is already solved and found in the database).
I get the following error:
Hi, sorry if my question is naive. But I would like to aks if it is possible to run the next command in multiple processors and not in just one?
relax.linuxgccrelease -s model1.pdb -nstruct 1000
and thank you
Hi, sorry for disturbing you but I have problems installing Rosetta. In Ubuntu 20.10.
I have also tried with clans, but it did not work. I follow all the classical error list, but still no success. Also I am not sure what is the error.
Could someone help me, please?