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Nucleic Acids

FARFAR2 error

Submitted by lijunnju on Tue, 2020-02-11 08:09
Category: 
Structure prediction
Nucleic Acids
ROSIE

Hi ROSIE and FARFAR2 team,

       I used FARFAR2 to test the 3D structure prediction of several RNAs two weeks ago with native PDB uploaded. But all the jobs were finally dead with the error message "2-rescore_to_native_or_lowest". Could you tell me why this happened? You can find the sequence, 2D structure, and native PDB in the attachment.

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ROSIE - General

Ligand question - aromatic bonds not being enforced?

Submitted by Rick_Baker on Wed, 2019-09-11 09:08
Category: 
Constraints
Small Molecules
Nucleic Acids

Hi,

I am trying to run Local Relax on an ADP-bound protein structure. I cleared the first hurdle to make a ligand params file, and the program runs fine and includes the ligand. I made the params file by taking ADP from a related structure, converted it to mol2 using iBabel, and made the params file using molfile_to_params.py

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Rosetta 3 - General

Installing rna_denovo

Submitted by Tanusree Chaudhuri on Thu, 2019-04-25 23:59
Category: 
Nucleic Acids

Hi,

I tried using the Rosetta RNA tertiary structure modeling pipeline as described in your article "Modeling complex RNA tertiary folds with Rosetta."

My build is correct.

But every time I try to run

helix_preassemble_setup.py -secstruct sec.txt -fasta fasta.fasta

I am getting error as

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Rosetta++ - Build/Install

Relaxing protein-RNA complexes

Submitted by rkirchdo on Fri, 2018-08-03 08:50
Category: 
Nucleic Acids

I'm new to Rosetta and I'm trying to relax a model of protein subunits bound to a short strand of RNA into cryo-EM density. However, I keep getting bad input errors on the RNA strand when I run this through relax and I would really appreciate some help. I have similar problems when I run the clean_pdb script which suggests to me that I'm not providing rosetta the correct instructions, the coordinates and residue names appear to be fine when inspected manually.

Thanks and Best wishes,

Rob

 

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Rosetta 3 - Applications

FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py

Submitted by obdulia on Wed, 2018-04-18 00:45
Category: 
Nucleic Acids

Dears,

After installing Rosetta 3.9 in a cluster and trying to run the simple command:

helix_preassemble_setup.py -fasta NFKB_1OOA_RNAStructure_2D.fasta -secstruct NFKB_1OOA_RNAStructure.secstruct

we get the following error:

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Rosetta 3 - General

Errors in Getting Erraser to run

Submitted by belousoff on Thu, 2017-06-01 16:13
Category: 
Nucleic Acids

Hey there,

I'm having trouble getting erraser to run. The following command:

erraser.py -pdb model_real_space_refined.pdb -map ../maps/FFT_13/70S_converted_1.ccp4 -map_reso 3.73

Give the errors as seen in the attached output.txt.

Everything compiled fine, using gcc5.4

any help would be appreciated.

 

cheers

 

matt B

 

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Rosetta 3 - Applications

constraints

Submitted by lah435 on Sun, 2017-03-12 03:25
Category: 
Nucleic Acids

My pose has DNA strands and I am trying to constrain the blunt ends.

Each DNA chain is numbered starting from 1. Why can't Rosetta find the atoms?

Here is my constraint:

AtomPair C1* 1C  C1* 35D  HARMONIC 12.028 1.00

And here is the error:

[ERROR] Exception caught by JobDistributor for job VGK8_v2_0001Atom 'C1* 1359' not found

 

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Rosetta 3 - General

calculate RMSD (RNA modelling)

Submitted by obdulia on Tue, 2016-07-05 01:58
Category: 
Nucleic Acids

Dears

With RNA modelling in Rosetta, how may i get the RMSD to a native structure for the whole set of generated models? I forgot to run the rna_denovo.linuxgccrelease with the -native flag and now, i would like to measure the RMSD for the obtained models (.out file) agaisnt the crystallographic structure.

Thanks a lot in advance

Best Regards

Obdulia

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Rosetta 3 - General

No RMS and IRMS values in protein/nucleic acid docking

Submitted by rbeier1 on Wed, 2016-01-13 12:41
Category: 
Docking
Scoring
Nucleic Acids

Hello,

I am docking a small protein / nucleic acid structure to generate dockings. The scoring contains only -nan for rms and 0.000 for Irms. Why doesn't the docking result in valid rms/irms values? Fnat and I_sc as well as total_score seem ok. What do I have to change in order to receive rms and irms values?

XML Rosetta Script (prot2.xml):

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Rosetta 3 - General

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