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Error while converting mol2 to params using molfile_to_params.py

Submitted by ahmadkhalifa on Thu, 2018-06-14 10:30
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. 

 

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PyRosetta - General

Multistate design on Rosetta - no generations produced

Submitted by tong on Wed, 2018-06-13 00:36
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

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Rosetta 3 - Applications

Relevant number of cycles of loop closure required

Submitted by vasavi on Mon, 2018-06-11 02:55
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.

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PyRosetta - Applications

GenericMonteCarloMover accept/reject moves

Submitted by ac.research on Fri, 2018-06-08 06:04
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)

 

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PyRosetta - General

RosettaDesign Result Evaluation

Submitted by ac.research on Tue, 2018-06-05 18:45
Category: 
Design

Hello everyone,

I wrote a script to perform RosettaDesign (both fixbb and flxbb) and I benchmarked it. Attached is the Abinitio folding simulation of three proteins, and my full script can be found here: https://github.com/sarisabban/RosettaDesign/blob/master/RosettaDesign.py

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PyRosetta - General

RosettaDesign improvements

Submitted by ac.research on Mon, 2018-05-14 08:27
Category: 
Design

Hello everyone,

 

I wrote a forum entry here (https://www.rosettacommons.org/node/10258) asking about details on RosettaDesign, and I am continuing the conversation here since I ran my script on several structures and got different results and I want a better understanding.

 

Please find attached a summery of the results. If you look closely you can see the green relaxed structure on the bottom left (sorry if it is not clear).

 

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Rosetta 3 - General

cartesian_ddg error: "Assertion `files.size() == 1` failed."

Submitted by cossio on Fri, 2018-05-11 09:59
Category: 
Design

I am trying to run the cartesian_ddg protocol (https://www.rosettacommons.org/docs/latest/cartesian-ddG).

I am using the following command: 

cartesian_ddg.static.linuxgccrelease \
 -database $ROSETTADB \
 -s min_2b5i-A_0001_clean_0011.pdb \
 –ddg:mut_file themutfile.txt  \
 -ddg:iterations 3 \
 -ddg::cartesian \
 -ddg::dump_pdbs false \
 -bbnbr 1 \
 -fa_max_dis 9.0 \
 -beta_cart

 

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Rosetta 3 - Applications

ab initio

Submitted by malkeet.singh on Thu, 2018-05-10 05:34
Category: 
Design

Hello!

 

I am using the standalone version of Rosetta, and so do for the Fragment picker application. in the tutorial, 3 SS prediction programs are used with weightage  of 0.6 for psipred and 0.2 each for other two programs; however, the Robetta server, produce results based on only 02 programs, i.e. psipred an Jufo so in this case, what is the weightage for both programs?

Thanks!
Malkeet

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Rosetta 3 - Applications

restrict PackRotamersMover

Submitted by pmit on Thu, 2018-05-03 01:48
Category: 
Design

Hello Everybody,

I'm using Rosetta to find a sequence that fits a given main chain using the fixBB or the PackRotamersMover. What I haven't been able to find out: How do I tell Rosetta to use the amino acid, which was selected by the alorithm for position X, also at position X+Y? In other words, the sequence should be identical at positions X and X+Y, but I would like to leave it to Rosetta to select a suitable residue and find suitable rotamers.

Thanks for your help.

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Rosetta 3 - General

Issue with Loop Analyzer Mover ouput

Submitted by abhi_pe_acharya on Mon, 2018-04-30 09:55
Category: 
Design

Dear Rosetta Users,

I am trying to design a loop present in a protein-protein interface. At the end of my design protocol, I inserted a LoopAnalyzerMover to assess the output decoys. To my dismay, I find very high LAM score, for all loop designs. An example LAM output is below:

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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Rosetta 3 - General

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