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Docking-RMS value nan

Category: 
Docking

Hello,

I am new to Rosetta3 and jsut trying to dock some generated ligands into a protein PDB. Based on the generated structures it appears the docking program is working well however, when I look at the score.sc file the rms vlaues for all the generated structures is nan. I do not really understand if I should be expecting rms values. I am docking a ligand into an unbound protein substrate. Any information would be helpful.

Justim

Post Situation: 

Error when trying docking protocol with different ligand

Category: 
Docking

Hi,

I'm coaching an iGEM team at the University of Warwick and they're doing some dock design to try to switch the specificity of a transcription factor to a different ligand. We've been able to run the docking protocol with the protein and it's native ligand and it is able to recapitualte the the native binding. However, when we try the docking protocol with the new ligand we run into this error:

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str::out_of_range with mpiexec and relax

Category: 
Scoring

I'm doing a very simple relax to optimize and score 100.000 pdb files.

Rosetta was compiled with MPI+MYSQL support. 

If I call the relax application on a single PDB file, it works.

Since I have a 64 core machine + 196 GB RAM (with MPI installed), I would like to relax 63 structures in parallel.
This is the command i'm executing with MPI:

mpiexec -np 63 /rosetta2020/main/source/bin/relax.mpimysql.linuxgccrelease @relax.flags.database

Post Situation: 

Trouble installing Pyrosetta

Category: 
Compilation

Hi, I had some problems downloading Pyrosetta (macOS 10.15.3 Catalina, python2.7.16, Pyrosetta-Release-2.7 from download page on website). After unzipping and running the setup command, I tried to import the pyrosetta library (import pyrosetta; pyrosetta.init() ) but got the error message

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "pyrosetta/__init__.py", line 15, in <module>

    import pyrosetta.rosetta as rosetta

Post Situation: 

Setting output values using a database (with relax app)

Category: 
Scoring

Hello all,

I noticed rosetta creates 23 tables in MySQL when using it as output backend in the RELAX application.

For my specific research I only need to hold the per-residue energies and the total energies... I don't need the atoms, topology or PDB data to be saved after each cycle, as it consumes a lot of memory.

Post Situation: 

BUG REPORT: MySql column protocol.protocol_id must have the AUTO_INCREMENT flag set

Category: 
Scoring

I tried running relax compiled with MPI and MYSQL.

MySQL was configured properly. A test run without MPI successfully created tables and wrote data to MySQL.
The protocol file @relax.flags was created with the following options:

-list pdblist.txt
-relax:script relax.script
-relax:bb_move false
-score:output_residue_energies
-score:weights res2015

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