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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!
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:
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!
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?
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
I am attemtpting to compile according to item 1.5.1 at https://csrosetta.chemistry.ucsc.edu/node/1354...
$ module load python/2.7 slurm openmpi/gcc/64
however slurm is not available. The cluster uses PBSPro. Can anyone suggest a work-around?
Thanks - Dave Morgan Ph.D., Colbert Lab, NDSU
I have a problem with cleaning my protein before ligand docking. I use the command clean_pdb.py 1i09 A to download and clean GSK-3, but the final structure has some missing residues, even more than the initial structure in the protein data bank. There is no gap in the AA sequence when open the structure as a text file, but using PyMol, there are dotted lines instead of solid lines in some areas of the structure. I have uploaded the initial and the cleaned PDB files for your consideration.