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Structure prediction

ETABLE constraint function type

Submitted by allan.ferrari on Tue, 2017-01-10 08:01
Category: 
Structure prediction

I am running rosetta_bin_linux_2016.15.58628_bundle and I would like to run a prediciton with a set of constraints which are defined by a potential using the ETABLE function.

As it was not implemented in the FuncFactory.cc file, I have added: 

#include <core/scoring/func/EtableFunc.hh> in the //Package headers

and 

FuncFactory::add_type( "ETABLE", FuncOP( new EtableFunc( 0, 0, 0) ) );

After that, I have recompiled and it worked to identify the Etable Function. :)

 

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Rosetta 3 - General

comparative modeling of a homodimer

Submitted by banshee on Mon, 2017-01-09 18:34
Category: 
Structure prediction

hello

i am trying to do comparative homology modeling of a dimer. does the input pdb have to have the dimer with both monomer threaded?

when i input a dimer pdb with grishin alignment file of the monomer i get a threaded pdb with only the monomer. can i use this pdb as the input pdb or do i need to thread the other monomer and add that to the input pdb? thanks!

oh and by the way is the robetta server down? thanks.

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Rosetta 3 - Applications

ArchiveManager -- spinning down

Submitted by Marius1987 on Fri, 2016-12-23 03:10
Category: 
Structure prediction

Hi Rosetta Community,

I am running RASREC CS-ROSETTA on a Cluster using 10 cores with mpi. 

After 2 days, I got this error message:

------------------------------------------------------------------------------------------------------------------------------------

ERROR: error detected in ArchiveManager -- spinning down

ERROR:: Exit from: src/protocols/jd2/archive/ArchiveManager.cc line: 445

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Rosetta 3 - Applications

Partial homology modeling in Rosetta

Submitted by al614 on Mon, 2016-10-31 12:30
Category: 
Structure prediction

Hello everyone,

I have a protein and I am only interested in modeling two parts of it, constraining the rest of the protein to the structure that we already know. I am new to Rosetta and would like to know what the best approach to this would be. 

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Rosetta 3 - General

Is the tools such as "r_pdb2top" "r_broker.linuxgccrelease" still available?

Submitted by zhiguang on Sun, 2016-10-30 19:00
Category: 
Structure prediction

Dear All:

 

I'm just begin to use Rosetta and following demos like " demos/protocol_capture/broker/ubq   " " demos/protocol_capture/topology_broker_gpcr "

 

Those examples call the "r_pdb2top"  "r_broker.linuxgccrelease" , however, it seems those no longer exist in the current version I got (rosetta_bin_linux_2016.32.58837_bundle)

 

It would be great if anyone knows which version still has those commands, or which commands has similar function.

 

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Rosetta 3 - Build/Install

Abinitio doesn't run but does not give output or error

Submitted by Irving on Fri, 2016-10-28 10:04
Category: 
Structure prediction

I want to predict the structure of an 85 residue protein, but every time I run abinitio the program stops with no errors or structure output. The protein has a known structure, and I've run abinitio on it successfully. When I remove the .pdb file the output below is all I get. Any suggestions would be greatly appreciated. 

My input:

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Rosetta 3 - Applications

span and frags filefor multichain transmembrane protein

Submitted by zhiguang on Wed, 2016-10-26 13:28
Category: 
Structure prediction

Dear All:

 

I'm quite new to Rosetta and I current got a problem when try to modelling a two-domain transmembrane protein.

 

The protein has two transmembrane domain (chain A, start from residue 1 and chain B, also start from residue 1). There is no covalent linking between the two domains.

 

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Rosetta 3 - General

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