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Submitting job to local cluster

Category: 
Design

Hi All,

I have installed rosetta on our institute cluster with mpi support (extras=mpi). I want to run rosetta script on the cluster (favor_native_residue.xml). Can anyone kindly let me know how to do it. Attached is a script i used to submit gromacs job in the same cluster (originally it was gromacs_job.sh but I changed it to gromacs_job.txt to attach here) and my favor_native_residue.xml (changed to favor_native_residue.txt for attachment). 

 

Thanks a lot.

 

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Give preference to native residue during fixed backbone designing

Category: 
Design

Hi,

I want to do fixed back-bone design. Rosetta output gives me a lot of mutation. I want to limit the numbers. I donot want mutations that marginally stabilizes the protein. Is there any way to tell to software to prefer the native aminoacid. 

 

Thanks a lot

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Errors in scorefiles after running Design

Category: 
Design

Hi,

I've successfully run Rosetta Design using the April 14th, 2014 weekly release (this is the latest weekly release that I can faithfully use, given the age of our cluster) on a large number of scaffolds. I've attached the options file (femoco2.txt) as a reference.

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RosettaScripts - SetupNCS mover

Category: 
Design
Constraints
Symmetry

Dear all

I was trying to mix ligand docking with protein design of a symmetric dimer by using the SetupNCS mover. I still don't know why the mover is not being used...the resultant pdbs were modified at the sequence level but both chains are different.

thanks in advance

felipet

 

The script used is:

 

        <MOVERS>

                <SetupNCS name=ncs bb=1 chi=1 symmetric_sequence=1>

Post Situation: 

Rosetta Design Stalling

Category: 
Design

Hello,

I am having problems with Design simply stalling at a specific step in a number of jobs I am running. I can recreate the error, but every time it happens the job stops here:

core.pack.task: Packer task: initialize from command line() 

I've checked the tasks of the computer I am running this on and it shows that Design is still running, and when I kill that specific job the Design run continues unperturbed. 

I've attached the appropriate log file. Any help would be greatly appreciated.

 

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Difference between movemap and -pivot_residues

Category: 
Design

Hello,

I'm debating whether I should use a movemap or the -pivot_residues flag to specify the flexible region in a backrub protocol. Movemap allows you to specify BB and CHI flexibility separately, but if I use BBCHI should I expect different performance vs -pivot_residues?

I would use -pivot_residues since it is simpler and I see examples recommending it here on the forum. However I'm comparing backrub performance to relax performance, and relax uses movemap but does not have the pivot-residues flag.

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Fusing C-terminal or N-terminal segments onto proteins using Remodel

Category: 
Structure prediction
Design
Loop Modeling

Hi I am trying to fuse a structure onto a designed protein structure at the C-terminus using the following command:

remodel.linuxgccrelease -s model3.pdb -remodel:RemodelLoopMover:bypass_closure -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -num_trajectory 3 -save_top 1 -database <PATH> -overwrite -out:file:scorefile model3.sc

model3.pdb covers the range: 1-393

model4 covers the range: 290 - 393

Where the blueprint has the following general format:

Post Situation: 

Fusing C-terminal or N-terminal segments onto proteins using Remodel

Category: 
Design
Loop Modeling

Hi, I am trying to replace the C-terminal segment of a designed protein with that taken from a crystral structure using the Remodel module with the DomainFusion flag turned on. I have tried several different tweaks to the arrangment however the gist of it is that I use the following command. 

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