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Running RosettaScripts, but got an error "src/utility/options/OptionCollection.cc, line 1153, No values of the appropriate type"

Category: 
Design

Hello,

I'm a new user wants to run a RosettaScripts with disulfize mover, but right after I start the scripts, I got the following crash report. Any comments or suggestions on how to solve the issues? Thanks a million.

Post Situation: 

An error occurred during the installation

Category: 
Compilation

Dear Rosetta Users,

I recentlly downloaded the src version of rosetta 2020.50 and compiled it with scons.py, but there was an error. It seems that the program was pointing towards a wrong directory (the bin version directory) for the generate_database_cache application. I'm attaching the log file. Thank you in advance!

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Remodel and the depracated EMPTY NC

Category: 
Design

I am using Remodel and I wanted to use a non-canonical amino acid. However, EMPTY NC XXX in the blueprint no longer works as I get an error (below), with a suggestion to use a PackerPalette via a PackerTask or TaskFactory.

I am using Remodel in Pyrosetta 4 2020.49 release (a stable)  for 3.7, but I believe my problem is Rosetta in general one, not a Pyrosetta one. RemodelMover does not accept a task. Furthermore, the pose index numbers change relative to the initial pose so I am not quite sure how such a task would look like.

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ERROR: Not complementary at positions

Category: 
Structure prediction

Hi Rosetta team,

    I am trying to generate some tertiary structures for a relatively large RNA (300+ nt) with rna_denovo. But I keep getting a strange error saying the nucleotides are not complementary:

[ ERROR ]: Caught exception:


File: src/core/pose/rna/RNA_SecStruct.cc:286
[ ERROR ] UtilityExitException
ERROR: Not complementary at positions C   48 and G   53
 

    I attached my secondary structure, fasta and ct file for the RNA. I wonder what's the cause of this problem. Thanks much.

Post Situation: 

de novo RNA loop

Category: 
Nucleic Acids

Hello, 
I'm using the rosetta rna de novo tool to generate a rna hairpin, I used the RNA_Denovo_with_base_pair_steps demo as a guide to do it, however I get the error: Atom C1' 1 not found. I' m newbie using rosetta so I would really appreciate any help or guide about the problem. Thank you!

Post Situation: 

Segfault with Pepspec

Category: 
Design

Hello,

I am using pepspec to design a peptide inhibitor of a serine protease. I am using a structure of the enzyme, with a docked Arg, obtained from a crystal structure (so no Anchor Docking is needed). I want to design a peptide by adding residues to the N-terminal side of the anchored Arg. Previous pepspec, I repacked the structure with fixbb with:

Post Situation: 

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!

Category: 
Membrane

I am doing an efficiency analylis on the different minimization options in Rosetta using FastRelax, MPRelax and lbfgs_armijo_nonmonotone minimizer on a membrane protein using the franklin2019 score function and I very very often get this error:

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!

Post Situation: 

cartesian delta delta G

Category: 
Design

Heya,

I am new to Pyrosetta and attempting to implement the Cartesian delta detla G paper, however i am struggling a bit with it. There is already a tutorial on delta deltaG in the official tutorials, and from my understanding the differences to the Cartesian version are simply an initial relax with a different score function (ref2015_cart) and then backbone relaxes around the mutation site. This is kinda what i am struggling with.

 

How can i relax only a certain site + 2-5 sites around it?

 

Post Situation: 

Segfault with docking protocol

Category: 
Docking

Hello,

I am trying to run the docking protocol for a high resolution local refinement, but I get a Segmentation fault error. The command is

docking_protocol.linuxgccrelease -partners A_B -docking_local_refine -database $ROSETTA_DB -in:file:l list.txt -ex1 -ex2aro -use_input_sc -out:file:silent decoys_high_res_refinement.silent -out:file:silent_struct_type binary -out:path:score score_high_res_refinement.sc -out:prefix high_res_ref_ -out:nstruct 100

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