The problem hasn't been solved
Hi
I am a beginner in pyroseta and now need to use pyrosetta to generate decoys of RNA with different RMSDs (e.g. 1Å, 5Å, 10Å), I checked the manual but it is still not clear, can you give me some guidance, thank you!
Hi , I'm beginner to Rosetta . In ligand_docking , it is said "chain_id F does not exist" . There are two ligands and one receport to dock , I can not define chain F or chain X (in my dock.xml). I can not undersstand some answers about this question. I wish receive the answer.
the process in ligand_docking:
Dear sir,
I am new to Rosetta. I followed the rosetta protocol to pad a few residues to N, C terminals of my protein. I follow the remodel.static.linuxgccrelease instructions. Created pad.bd as below. Then I run "rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/remodel.static.linuxgccrelease -in:file:s 1mhp_H_0001.pdb -remodel:blueprint 1mhp_padpadded -remodel:dr_cycles 1 -num_trajectory 1 -save_top 1" . but it only added Val reisidues. I want to added non-specified residues but not all into VAL. how to fix this? Kind regards.
Previously, I want to add spin to the "Initial Perturbation" on protein-protein docking (https://www.rosettacommons.org/node/11700), and I with the second partner spin around the axes of the center of the two ligands. I think using AtomTree can set a jump between the two ligands, so I introduced the SpinMover to control the rotating axis. Can the jump be set between two ligands? Because I got an error when running with modified FoldTree:
I am a beginner to rosetta, and I was wondering if there is a way to truncate/ get rid of a specific part of a sequence and create a stable protein? I have the PDB of the protein and the specific parts of the sequence I need to truncate. It is to get rid of loops at the terminus. Do I just input a sequence to rosetta with the unwanted parts deleted and have it model the protein ?
Sequence :
G-SPELREKHRALAEQVYATGQEMLELREKHRALAEQVYATGQEMLKN-TSN
I am running loop model with the remodel protocol (remodel.static.linuxgccrelease). It succesfully can model despite ligands in the file using -ignore_unrecognized_res when a single structure is required with -nstruct 1 however as soo as I try to increase it to -nstruct 2 I get a segmentation fault. Anyone experience this before?
Hi all
I'm trying to dock the ligand into receptor with rosetta ligand docking with following command line
mpirun -np 20 rosetta_scripts.mpi.linuxgccrelease @options
where options file looks like this
Hi all,
I am new to Rosetta and FARFAR2. I have attempted modelling the structure of PDB:1KXK using the following command line:
rna_denovo -sequence gucuaccuaucgggcuaaggagccguaugcgaugaaagucgcacguacgguucuaugcccgggggaaaac -cycles 20000 -nstruct 3 -bps_moves false -minimize_rna true -secstruct ".....(((.((((((...(((((((((((((((....))))))..)))))))))..)))))))))....."
Now I want to compare the obtained structure to the original PDB and to calculate the RMSD. I ran the following:
