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:
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
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
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
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):
I tried to generate Protein/Nucleic acid - Decoy structures using Rosetta, but failed in the low-resolution docking protocol. It seems to be a similar problem as already mentioned in no-output-pdb-files-after-docking-protein-and-dnarna.
Hi,
I am trying to run the protein-RNA interface design protocol present in rosetta_demos. I found that in the xml file the residues that are allowed for design are not present in the protein (1a9n_ABQ). Am I missing something here ??
I also want to know whether rosetta can score protein-RNA interactions well or not, and what extra terms are scored in calculating the binding energy of the designed interface in case of protein-RNA interactions?
Is it possible to combine a flags file with command line arguments?
For example, something like this:
minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file
where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:
minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list
Thanks.
I have run into an intermittent problem with RNA_minimizer within the rna_denovo application. I am using identical setups in different directories and shells. I have two calculations currently running without problems. When I try the same calculation in a 3rd directory, I am getting high scores for lk_nonpolar and the resulting pdb structures have steric clashes with overlap side chain atoms. There are no errors reported during the calculation, but the results are not usable.
The calculation is a simple rna hairpin using rna_helix to generate the stem.pdb file:
