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RosettaDesign error with Option file open failed

Category: 
Design

Dear users and developers,

I was running RosettaDesign and an error was reported as "[FILE]: src/utility/options/OptionCollection.cc

[LINE]: 536

[START_MESSAGE]

Option file open failed for: '/**/general_FD.flags'".  

This flag file worked on other server previously. Is this an error with compiling Rosetta or with the flag file? Could anyone please give some suggestions about how to fix this? Thank you so much.

Best,

Post Situation: 

Error when trying to thread target sequence over template pdbs, partial_thread.static.macosclangrelease not working properly

Category: 
Design

*** note sure which category was appropriate for my question, chose Design but my Q pertains to threading for RosettaCM module***

Hello everyone,

Post Situation: 

Error when compiling in Linux Ubuntu VM

Category: 
Compilation

Hi, good day everyone, 

I was trying to compile Rosetta 3 and after running smoothly for two hours it stopped, and I got the following error message: 

g++: internal compiler error: Killed (program cc1plus)

Please submit a full bug report,

with preprocessed source if appropriate.

See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.

scons: *** [build/src/release/linux/5.3/64/x86/gcc/7/default/core/io/pose_from_sfr/chirality_resolution.os] Error 4

Post Situation: 

How to add my own .cc and .hh file

Category: 
Compilation

Hello,i use scons to complie.

Recently,I write some class in .cc and .hh files , when i #include<~path/name.hh>,i find that it did not compile .cc files. I have read sconstruct file but do not know how to add my own file to compile with.

Please give me some help

Post Situation: 

Relaxation vs minimisation

Category: 
Structure prediction
Scoring
PyRosetta

Hi all,

I am very new to the computational structural biology community and I have tried to model a structure by using a software which runs MODELLER on the background. However, my result shows a number of steric clashes and a very high fa_rep when I calculate it with PyRosetta. I am therefore trying to improve the structure before moving on with the rest of my analysis. 

Post Situation: 

antibody_numbering_converter cannot recognize the IMGT scheme

Category: 
Docking

To whom it may concern:

Hi I want to convert my antibody structure from Chothia to IMGT. I use the following command and get an error "ERROR: Illegal value specified for option -antibody:output_ab_scheme : IMGT". I am wondering is the IMGT scheme already cancelled in the number converter program? This is a 2019.35.60890 version.

/home/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_numbering_converter.linuxgccrelease -input_ab_scheme Chothia -output_ab_scheme IMGT -s 1ahw_chothia.pdb

 

Best regards,

Post Situation: 

MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"

Category: 
Design

Hello everyone,

I am trying to use MotifGraft mover to graft an epitope to a scaffold protein (actually there is a structure library, parsed with -l list).

The xml script is attached.

My command line is as follow (I am first trying a very loose boundary conditions, I'm aware about the higher RMSD/atom_clash values):

Post Situation: 

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