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Parametrisation problems

Submitted by DmitriiN on Tue, 2016-05-31 09:37
Category: 
Design

Hello everyone!

I have a residue in my protein, that is non-canonical and that I named REL.

After all the steps from https://www.rosettacommons.org/demos/latest/public/design_with_ncaa/README with the only difference in using molfile_to_params.py instead of molfile_to_params_polymer.py, because the second doesn't work in my rosetta suite.

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Rosetta 3 - General

-RBSegmentRelax:cst_wt not present in ca_to_allatom.linuxgccrelease application?

Submitted by Karol on Thu, 2016-05-12 06:30
Category: 
Design

 Hey,

I am using Rosetta to build my protein from Ca-trace to all-atom, and then to refine this structure against cryo-em density.

However, when I use these two flags:- RBSegmentRelax::cst_wt 1.0  and -RBSegmentRelax::cst_width 4.0, I am getting the error:

Option matching -RBSegmentRelax:cst_wt not found in command line top-level context. 

When I remove these two flags, everytging works perfectly.

So, my question is: do these two flags are still used by ca_to_allatom application?

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Rosetta 3 - General

Submitting job to local cluster

Submitted by tusharranjanmoharana on Fri, 2016-04-15 01:38
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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Rosetta 3 - General

Give preference to native residue during fixed backbone designing

Submitted by tusharranjanmoharana on Mon, 2016-04-04 12:43
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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Rosetta 3 - General

Errors in scorefiles after running Design

Submitted by Jhreed on Tue, 2016-03-29 10:25
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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Rosetta 3 - General

RosettaScripts - SetupNCS mover

Submitted by felipet on Fri, 2016-03-25 12:42
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>

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Rosetta 3 - Applications

Rosetta Design Stalling

Submitted by Jhreed on Sun, 2016-03-06 14:38
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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Rosetta 3 - General

Difference between movemap and -pivot_residues

Submitted by aloshbau on Wed, 2016-02-24 13:21
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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Rosetta 3 - Applications

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