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Installing pyrosetta for proteinmpnn use

Category: 
Design
PyRosetta

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.


 

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protein-protein docking

Category: 
Docking

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

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FARFAR2 Error With Secondary Structure File

Category: 
Nucleic Acids

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]

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JD3 w/ Silent file output crashing - Option filename not found

Category: 
Scoring
<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>

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ERROR: Assertion `build_sets_[ build_set_id ].restype().has( "1HA" )` failed. ERROR:: Exit from: src/protocols/match/upstream/Pr

Category: 
Docking

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).

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Academic email verification

Category: 
ROSIE

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

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Academic Email Verification

Category: 
ROSIE

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

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