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Errors in Interface_design_demo

Category: 
Design

Hello there,

When I try to run the minpac_optE-premin under interface_design_demo, I got the following error message:

File: src/utility/options/OptionCollection.cc:239
ERROR:

File: src/utility/options/OptionCollection.cc:1324
Option matching -corrections:score:hb_sp2_peak_heigh_above_trough not found in command line top-level context

[ WARNING ] Tried to calculate the visibility of Tracer 'Error' before init() was called!
[ WARNING ] This tracer will not obey commandline options.

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Error when using RabD with a nanobody.

Category: 
Design

Hi Everyone,

Recently, I am using RabD to design my nanobodies, But I can not perform it smoothly:

 

>>>Error returns:

ERROR] Exception caught by JobDistributor for job complex.1_0001

 

File: src/protocols/antibody/AntibodyInfo.cc:1117

 

L1 start resnum not found in pose: 24 L

Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB.

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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).

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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: 

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:

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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: 

rosetta backrub

Category: 
Design

Hello

I want to use Rosetta backrub for peptide design. by I faced an error that I think it caused to incompatible .py and .sh files and Rosetta 3.9 2018 version. I searched a lot on Rosetta website to find out any example of .py and .sh file that they need for running Rosetta Backrub. my error was ERROR: unable to open MM atom type  set file:/home/nanobio/amin/rosetta_database/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt ERRoR: Exit from: src/core/chemical/MMAtomTypeSet.cc line 64".

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