Hello,
I have downloaded a PDB with a chemically bound ligand (small molecule)
I have followed (in every way that I can see) all the details presented in the tutorial/demo here:
https://www.rosettacommons.org/demos/latest/public/relax_around_chemically_bound_ligand/README
Hi,
I am trying to reproduce the the results from this paper 'Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps', but when I try to run the script from the paper (de3mo) i'm getting the following error:
File: src/utility/options/OptionCollection.cc:1467
Option matching -in:file:override_database_params not found in command line top-level context
I am working with a protein with a bound small molecule (non-covalent). I've managed in creating parameters for the ligand and relaxing the complex following this workflow: https://new.rosettacommons.org/demos/latest/public/relax_around_chemically_bound_ligand/README
Hi, I am having trouble minimizing a protein that contains trehalose. Unfortunately, Rosetta does not like trehalose and always deforms it.
I have no problems with glucose, that's weird because trehalose is a glucose disaccharide. I am using the flag -include_sugars and the relaxed structure has unrealistic energies because it forces the formation of non-existing bonds. The main problem is that rosetta assumes it is ->2)-alpha-D-GlucP
Dear all,
I want to relax a protein with a ligand in a specific position using the simple "relax.linuxgccrelease" program. However, I found that if the atom names (third column at the PDB) are not as expected, the output "relaxed" PDB shows a weird ligand (it looks more like an insect than a molecule), regardless if the ligand is already parameterized in Rosetta (Sorbitol [SOR] in this case). Once the atom names are fixed, the relaxed structures make sense.
Hi,
I have been trying to perform Ligand Docking with the ROSETTA software. I describe what I have done:
1. First, I have the ligands in sdf/mol2 format one per file. I add hydrogens to these and create the params files with the "molfile_to_params.py" script.
2. Second, I clean the protein (no ligands or cofactors) and add H to the protein.
3. Third, I concatenate the protein with each ligand in a different file for each ligand (the ligand has chain identifier X, the protein A).
Hi, I'm minimizing structures in a list of PDB's using the -l option. Some structures have different ligands which I'd like to ignore or skip. The -ignore_unrecognized_res doesn't work. Minimize got bumped out trying to fill in missing atoms. Apparently it did not see or understand the flag.
Hi Steven, Rocco, et al.,
I'm trying to use pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader for a project of side-chain packing small peptides with a fixed backbone. I've gotten as far as building the Mover: instantiate the mover, giving it rebuild info and the string with selected rotamers.
The problem I run into comes when I try to apply it to the starting pose; I get a warning:
