Error with docking_prepack_protocol while executing the tutorial "Docking Flexible Proteins"
Hello!
I'm new at Rosetta and was doing the tutorials for protein-protein docking. I execute the command below with no problems:
The problem hasn't been solved
Hello!
I'm new at Rosetta and was doing the tutorials for protein-protein docking. I execute the command below with no problems:
What is the best way to install PyRosetta for use with Protein MPNN? I am installing it for myself on an hpc cluster (redhat linux 8) and haven't found much documentation outside of that for the general PyRosetta install.
I'm doing protein-protein docking, in which the C-terminus of one of my protein chains (PDB: 2ew4) was amidated, and when I submitted it to Rosetta and ran docking_protocol.static.linuxgccrelease, I found that the amide was automatically disassembled, how can I make it so that it doesn't happen?
2ew4_ 1.pdb is the structure before docking, 2ew4_ 2.pdb is the structure after docking
Any help with the following error? Thank you
--------------------------------------------------------------------
[FILE]: src/core/pose/rna/RNA_SecStruct.cc
[LINE]: 139
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Number of right brackets does not match left brackets
[END_MESSAGE]
[END_CRASH_REPORT]
<Job nstruct="5">
<Input>
<PDB filename="pdb_basename.pdb" />
</Input>
<Output>
<SilentFile path="pdb_basename" filename="pdb_basename_relaxed.silent" />
</Output>
<SecondaryOutput>
<ScoreFile path="pdb_basename" filename="score_pdb_basename.sc" />
</SecondaryOutput>
<Options>
<parser__protocol value="path/to/RELAX_MONOMER_RS" />
</Options>
</Job>
Hi Rosetta community,
Hoping someone can help me with this issue I'm having! I'm trying to dock a cofactor and a ligand into an alphafold model using Rosetta match. Essentially, I know which residue is supposed to be covalently bound to the cofactor, so I've made that the first constraint block of the CST file. Then, I am trying to match the ligand with the cofactor. This is constraint block #2 and as such I have included the following lines at the end of CST block 2 (since I'm matching essentially ligand 1 to ligand 2).
There is a unbind function:
Hi,
Could you please verify my academic email address so that I can access ROSIE via Github?
My institution name: Research Center in Food & Development (CIAD) in Mexico.
Institution domain: @estudiantes.ciad.mx
Thanks in advance!
Hi,
Could you please verify my academic email address so that I can access ROSIE via Github?
My institution name is Casa Sollievo della Sofferenza Hospital. I work in the unit of Medical Genetics and I do not-for-profit research in rare diseases.
My institution domain is @operapadrepio.it
Hello,
I am unable to login to ROSIE with my GitHub account. I have provided my institutional email ID. I study at Tata Institute of Fundamental Research, India. The institutional domain address is 'https://www.tifr.res.in/'. My email address domain is '@tifr.res.in'. Please help me out. Thank you!
Shahina Mazumdar Research Scholar Dr. Debasis Das's Lab Department of Biological Sciences Tata Institute of Fundamental Research Colaba, Mumbai - 400005 Email: shahina.mazumdar@tifr.res.in