You are here

Unsolved

The problem hasn't been solved

Rosetta script to relax a neighborhood only

Category: 
Design

I often have a disruptive mutation, say a selection winner has leucine to a proline, where design, backrub and even Remodel (with finding neighbours) give a pose with an empirically discordant poor score. Doing a Relax fixes things, but relax is dangerous as it is may find a better minimum for an unrelated loop (say as a helix).

Post Situation: 

ProteinInterfaceMS

Category: 
Design

Hello,

I have been running the ProteinInterfaceMS mover with rosettascripts. It runs successfully, though one single design seems to take about 5 days to complete. This is on one cpu. I was wondering if ProteinInterfaceMS mover is capable of making use of MPI? If so how does it split the calculations? And how would you submit the command?

 

Thanks

Post Situation: 

Multistage_rosetta_scripts

Category: 
Compilation

Hello,

 

I would like to try the multistage_rosetta_scripts protocols. Unfortunately when I build rosetta the multistage_rosetta_scripts.XXX.release doesn't build.

I am a commercial user. Is this feature available for commercial users. I even downloaded the newest weekly release, 42.

 

Thanks

Post Situation: 

Predicting the part of protein strcutrue

Category: 
Structure prediction

Hi,

I have a protein whose sequence is fully known and whose structure is partial known. Most sequences of the protein are folded in the luminal ER domain and this part is resolved by experiments. However, transmembrane and cytosolic parts of the same protein are not resolved. As only the luminal part of the protein is resolved, I would like to predict the structure for transmembrane and cytosolic domains. Is there a way to predict only these parts while I keep the experimentally-resolved luminal domain?

Thanks, Siyoung

Post Situation: 

DockingProtocol mover ensemble error

Category: 
Docking

Hi all,

I would like to know if the mover DockingProtocol allows the use of ensemble for running docking with RosettaScripts.

I have an ensemble for both protein partners and I have used the flags -ensemble1 and -ensemble2.

If I use the DockingProtocol mover (script file test1.xml attached) aparently it does not turn ON the ensemble flag and I get an unexplained error:

 

...

Post Situation: 

Error in enzyme_design.default.linuxgccrelease: corrupted size vs. prev_size

Category: 
Design
Enzyme Design

Dear Rosetta Team,

I am trying to run enzyme design protocol on protein model with 2 Iron ions, 2 Ions, 1 molecule and 1 water molecule (!). Problem is it is getting core dump/segmentation fault each time I run it. After various code recompilations and printing the error I came came to know the error is at "EnzdesBaseProtocol::enzdes_pack(" in EnzdesBaseProtocol.cc.

code:

Post Situation: 

cartesian_ddg output

Category: 
Design

I am following the protocol

https://www.rosettacommons.org/docs/latest/cartesian-ddG

to predict the ddG of a monomer after a point mutation. I am using Rosetta 3.10.

The output file, mutfile.ddg, looks like this:

COMPLEX:  Round1: WT ...

COMPLEX:  Round2: WT ...

COMPLEX:  Round1: MUT_1ALA ...

etc.

Instead of COMPLEX, I was expecting to see lines beginning with

BEFORE_JUMP: RoundX:

Post Situation: 

Warnings during relax

Category: 
Design

I am getting  a lot of warnings like this:

core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 53 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 92 BRANCH 1
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
 

This is using the following relax command:

Post Situation: 

Pages