You are here

Unsolved

The problem hasn't been solved

READ THIS BEFORE YOU POST

When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation: 

The question about ligand score function

Category: 
Small Molecules

Hello!

These are many .wts file in database\scoring\weights.
I  don't clearly know which weight is used in which occasions,
and  just use score function according to papers.


I  read the webpage(https://www.rosettacommons.org/demos/latest/tutorials/scoring/scoring)
 and its recommend references.

Post Situation: 

ERROR: Unused "free" argument specified: GDP.fa.tors

Category: 
Structure prediction

I have the following flags in my refinement flag file, I'm getting the error ERROR: Unused "free" argument specified: GDP.fa.tors, I'm not sure why! 

-extra_res_cen GTP.cen.params GDP.cen.params -extra_res_fa GTP.fa.params GDP.fa.params-extra_improper_file GTP.fa.tors GDP.fa.tors 

 

Post Situation: 

Error while converting mol2 to params using molfile_to_params.py

Category: 
Structure prediction
Docking
Design

I'm trying to run python /home/labusr/rosetta/main/source/scripts/python/public/molfile_to_params.py --keep-names --clobber --extra_torsion_output --centroid gtp.mol2 -p GTP -n GTP, on a gtp.pdb that has been reduced using phenix.reduce and converted to mol2 using openbabel. Below is the error I get. 

 

Post Situation: 

Multistate design on Rosetta - no generations produced

Category: 
Design

Hi,

I am currently running a multistate design protocol (mpi_msd.linuxgccrelease) for bispecific antibody design. After I have run the protocol with my options, the program runs and is "stuck" at this point for a long time:

core.pack.pack_rotamers: built 39485 rotamers at 58 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DoubleLazyInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 22325380 bytes

Post Situation: 

The question of ligand docking with constraints

Category: 
Docking

Hello,

I read the paper Rosetta and the Design of Ligand Binding Sites

and it enlightens me.

According to the method of this paper,  I design my enzyme.

However,  I find these are a few unreasonable results which show reaction atom of ligand  do not close to  catalytic triad,

but  the opposite side of ligand close to  catalytic triad.

So I want to  make docking with  constraints

Post Situation: 

Relevant number of cycles of loop closure required

Category: 
Structure prediction
Design
Loop Modeling

Dear All,

I have been working on the Domain insertion module of Rosetta. I need to know what are the relevant number of cycles of loop closure I require to enter for larger domain sets. The domain Im inserting is around 175 aa long. I am having trouble launching the same using MPI in parallel, hence the single processor is taking days for the output. Wondered if anyone who has worked on it could suggest a feasible number for AnchoredPDBcretator and also for AnchoredDesign.

Vasavi.

Post Situation: 

GenericMonteCarloMover accept/reject moves

Category: 
Design

Hello People,

I have setup a generic montecarlo mover with backrub, but I do not get any accepted nor rejected moves, the following is my code:

backrub = pyrosetta.rosetta.protocols.backrub.BackrubMover()
backrub.pivot_residues(pose)

GMC = pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover()
GMC.set_mover(backrub)
GMC.set_scorefxn(scorefxn)
GMC.set_maxtrials(500)
GMC.set_temperature(1.0)
GMC.set_preapply(False)
GMC.set_recover_low(True)
GMC.apply(pose)

 

Post Situation: 

Pages

Subscribe to RSS - Unsolved