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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:
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
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
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.
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:
Dear users and developers,
I was running RosettaDesign and an error was reported as "[FILE]: src/utility/options/OptionCollection.cc
Option file open failed for: '/**/general_FD.flags'".
This flag file worked on other server previously. Is this an error with compiling Rosetta or with the flag file? Could anyone please give some suggestions about how to fix this? Thank you so much.