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dock & design

Submitted by sdh_h on Fri, 2016-09-02 03:07
Category: 
Docking
Design
Constraints
Symmetry

Dear All,

I would like to simultaneously dock and design two (or more) identical subunits into a a symmetric homooligomer.

Input:

- backbone structure of a monomer (no sidechains!);
- initial arrangement of the subunits;
- constraints that precisely define interactions between the subunits.

Simulation:

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Rosetta 3 - General

sequence_tolerance is very slow when -ms:num_packs > 1

Submitted by coomteng@gmail.com on Thu, 2016-08-25 13:17
Category: 
Design

Hi,

here is the command I used. When I set num_packs to 1 which is the default value, the program runs pretty fast, when I set it to other values, the program is stuck there. The version is rosetta 3.6.

 

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Rosetta 3 - General

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

"Illegal Instruction" for particular Movers/Filters

Submitted by Jhreed on Thu, 2016-08-11 12:59
Category: 
Design

Hi everyone,

I'm attempting to use a script involving a number of different components, but have run into a certain issue.

When I intiate the mover using the attached XML file "design.txt" (which is renamed design.xml when running the script), I get an error of:

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - pack=======================
Illegal instruction

The full log is attached (designerr.log).

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Rosetta 3 - General

BridgeChainsMover

Submitted by msardejani on Sun, 2016-08-07 17:32
Category: 
Design
Scoring
Loop Modeling

Hi,

I am using the 2016.28 build and have the some problems with "BridgeChainsMover" from Brian's recent method paper: DOI:10.1007/978-1-4939-3569-7_20

I get this error "ERROR: 'scorefxn' is not a valid option for BridgeChainsMover".  Here is the part of script that returns an error:

<BridgeChainsMover name="connect" chain1="1" chain2="2" motif="3LX-3LA-3LX" overlap="3" scorefxn="centroid_scorefunction" />

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Rosetta 3 - General

[Mover] is not known to the MoverFactory

Submitted by Jhreed on Fri, 2016-08-05 12:23
Category: 
Design

Hi,

I'm running the 2016.20 weekly release of Rosetta and am running into some issues.

The bottom line is that this error comes up when I attempt to use certain Movers:

Error: ERROR: Exception caught by rosetta_scripts application:FastDesign 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)?
Error:

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Rosetta 3 - General

Enzyme Design with additional covalent backbone bonds

Submitted by mwfranklin on Wed, 2016-08-03 10:23
Category: 
Design
Enzyme Design
Constraints
Non-Canonical Peptides

Hey everyone,

I am trying to design a protein with a covalent bond between the C of Thr and the N of Gly with a Tyr in between them (imitating the chromophore from GFP for perspective). Because of this odd 5-membered ring formation, I used Thr/Gly with a generous distance constraint between them in my CST file when I ran RosettaMatch to find likely sites in my scaffold proteins. My sites place the two backbone atoms ~4-5A apart.

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Rosetta 3 - Applications

Modeling protonated histidine

Submitted by SenyorDrew on Mon, 2016-07-18 07:34
Category: 
Design

Hi,

I'd like to model one of the histidines in my structure to be in a protonated form with hydrogens on the NE2 and ND1.  I see there's a param file for protonated histidines (~/rosetta/database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states/HIS_P.params).  What's the best way to specify in my pdbfile that I want that particular histidine to be protonated?

 I tried renaming the residue to "HIP" in my pdbfile and changing the first few lines of that param file to be:

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Rosetta 3 - General

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