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Segmentation fault (core dumped) in rosetta_scripts.default.linuxgccrelease after blueprint file reading

Category: 
Design

Dear Sir and Madam,

When I run such a script "~/rosetta_src_2020.08.61146_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol Design.xml -s some_relaxed_protein.pdb -database ~/rosetta_src_2020.08.61146_bundle/main/database/ -restore_talaris_behavior true -remodel:use_pose_relax true -score:set_weights pro_close 0 cart_bonded 0.5 -nstruct 10 -out:prefix design_" for insertion one amino acid, replacement one original amino acid into another and building additional disulphide I meet with the following error:

"[FILE]: SIGSEGV

Post Situation: 

"core.kinematics.FoldTree" error upon running RAbD

Category: 
Design

Dear all, 

I am trying to running RAbD with the following command:

antibody_designer.linuxgccrelease \
   -l design_input.list \
   -primary_cdrs H3 \
   -graft_design_cdrs H3 \
   -seq_design_cdrs H1 H2 \
   -do_dock \
   -paratope H3 \
   -mc_optimize_dG \
   -mc_total_weight .001 \
   -mc_interface_weight .999 \
   -out:path:all designing\
   -out:file:scorefile designing_scores.fasc\
   -nstruct 3 | tee designing.log

Post Situation: 

How to choose designed antibody

Category: 
Design

Dear all,

I am trying to use Rosetta dock and antibody design modules to design antibody in order to improve the affinity of the antibody to the antigen.  Firstly I docked the antibody to the antigen. In this step I got 500 and antibody-antigen complex models and selected top 10 models based on the lowest I_sc energy. Then I ran AntibodyDesign using a command like the follow for each of the 10 complex models:

Post Situation: 

Coupled Moves crash with Membrane Protein - residue_edge is undefined for root vertex

Category: 
Design
Membrane

Hi All,

I came across the Coupled Moves protocol recently and it sounds like an interesting alternative to FastDesign that I've been predominantly using. I tried to implement the CoupledMoves Mover within my RosettaScripts design script, however, I keep coming across the following error:

ERROR: FoldTree:: residue_edge is undefined for root vertex
ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 2317
[0m[0mprotocols.rosetta_scripts.ParsedProtocol: [0m[31m[1m[ ERROR ][0m Exception while processing procotol: 

Post Situation: 

Difference between interface_delta_X and dG_separated?

Category: 
Design

Hi, everyone!

I am using RosettaLigand design protocol to design some mutants, in order to improve binding affinity to a small molecule. When I was using InterfaceAnalyzer, there were 2 values representing binding affinity, interface_delta_X and dG_separated. I want to know the difference between these 2 values and which one I can use during the filter process.

Any suggestion will be appreciated!

Nicole

Post Situation: 

Building loop extensions in a membrane protein with Remodel

Category: 
Design
Scoring
Loop Modeling
Membrane

Hi All,

I was wondering whether Remodel is currently compatible with the RosettaMP framework? I have a designed membrane protein and I'm trying to alter the sequence of water-exposed loops, which involves a few insertions. I'm using Remodel to do this but haven't been able to run it using the franklin2019 scorefunction.

Here are the flags that I'm using:

Post Situation: 

mp_transform optimize with franklin2019 scoring

Category: 
Design
Scoring
Enzyme Design
Membrane

Hi All,

I am running some flexible backbone design on a transmembrane four-helix bundle heme protein via RosettaScripts. I'm finding that the membrane residue is moving a lot during design, and I have to optimize the embedding with mp_transform post-design to reposition the mem residue. I have a few questions about this:

Post Situation: 

RosettaAntibodyDesign: How can I run the protocol without allowing design?

Category: 
Structure prediction
Docking
Design

Hi there,

I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb. 

However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).

Is there any way to runn RAbD while FIXing all the CDRs?

Post Situation: 

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