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relax - P6G molecule

Submitted by allan.ferrari on Wed, 2016-11-30 05:01
Category: 
Small Molecules

I would like to relax some decoys with a small molecule, P6G, in a specific location, extracted from a homologous protein from PDB. For doing so, I have saved a PDB file with the protein as chain A and P6G as chain B. Rosetta does not recognize P6G as a residue, for obvious reasons.

Is there a straightforward way to run the relax protocol in this situation?

 

Best,

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Rosetta 3 - General

Symmetric design with PyRosetta

Submitted by dsim on Thu, 2016-11-17 07:50
Category: 
Design

Hello,

 

Is it possible to do symmetric design with PyRosetta4 ?

 

I try to pass a symmetry flag to the command line and run pack_rotamers but I get a warning saying that I try to

use a symmetric score function on a non symmetric protocol or something like that.

 

In previous Rosetta versions, there was a symmetric_pack_rotamers, but this method disappeared and there is some symmetry code in

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PyRosetta - General

lysine-aspartate isopeptide bond

Submitted by matteoferla on Tue, 2016-11-01 10:54
Category: 
Constraints

Hello,
I am working with protein which have isopeptide bonds in them and I am not sure how to handle them.

An isopeptide bond is when a lysine residue forms an amide bond with an aspartate or asparagine (same result). Isopeptide bonds —in bacteria at least— have an O or N atom missing from the Asp, Asn or Lys and a CONECT at the end of the file and to the best of my knowledge there is no special HETATOM O-lysylaspartyl double residue.

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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

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

Relaxing experimental structure

Submitted by aloctavodia on Thu, 2016-09-29 03:46
Category: 
PyRosetta

I need to measure the Rosetta "energy" of a set of conformations taken from the PDB. Before computing the energy I would like to relax the structures while keeping them as close as possible to the experimental structure. I guess I want something like this. Is that protocal available using PyRosseta? Or I should try to "implement it" my self.

I guess I could do something like:

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PyRosetta - General

'MPI' has not been declared

Submitted by starone on Wed, 2016-09-21 07:49
Category: 
Compilation

Hello,

I have built the MPI binaries many times without issue... until now.  I have two machines with the same Ubuntu build, openmpi, and site.settings file on them.  The build goes fine on one, but fails on the other (I did the openmpi installation tests and they succeed).

In the build output I see: "'MPI' has not been declared".   Below is more of the output... thank you very much in advance for your time!

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Rosetta 3 - Build/Install

RMSD calculation

Submitted by hamedkhakzad on Tue, 2016-09-13 04:56
Category: 
Scoring

Dear all,

Hi,

I need help with Ca-RMSD calculation. I've used docking protocol to generate some models and now I want to calculate Ca-RMSD between these models and the native. Each model has 5 chains: e.g. model_AB_CDE. I want to calculate Ca-RMSD in a way that the model_AB chains would be aligned on native_AB and the RMSD between model_CDE and Native CDE will be computed. How can I do that? I've used score protocol but it computes the total RMSD between all the chains.

Thanks in advance,

Best,

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Rosetta 3 - Applications

HBNetStapleInterface

Submitted by sdh_h on Wed, 2016-08-24 03:30
Category: 
Design

Hello,

is HBNetStapleInterface avaliable in the current version of Rosetta?

In 2016_15 build i get:

Error: ERROR: Exception caught by rosetta_scripts application:HBNetStapleInterface is not known to the MoverFactory. Was it registered via a MoverRegistrator in one of the init.cc files (devel/init.cc or protocols/init.cc)?

Best wishes,

Staszek

 

 

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Rosetta 3 - General

Is the packer aware of non canonical amino acids?

Submitted by krdav on Tue, 2016-08-16 08:16
Category: 
Design

I am having a problem when setting the packer to design residues that are non canonical in the pdb file I provide. I have an example for 2ovq where the short peptide called chain C has two phosphorylated residues (TPO at 380 and SEP at 384). When I make a resfile like this:

NATAA
start
384 C ALLAA

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Rosetta 3 - General

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