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I'm trying to dock my ligand with HEM to CYP using rosetta script with XML protocol
overall running process seems to complete without any problem, and rosetta script seems to recognize HEM and ligand as separate entity
But in some conformer generated by rosetta-script, there is severe clash between HEM and ligand.
For this kind of conformer, rosetta total_score was extremely high and I could filter out this kind of unfavorable structure based on rosetta score
I'm attemping a docking run with a protein that acts on an amino acid substrate. (tyrosine) Whenever I initiate the run it gives me the warning:
[ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 1 W TYS TYR:CtermProteinFull:NtermProteinFull:sulfated
core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA .
And then the error:
[ ERROR ]: Caught exception:
chain_id W does not exist
Dear Rosetta Users,
I have an ensemble of protein conformations obtained by means of MD (Molecular Dynamics) simulation.
I would like to know if a recent protocol is available to dock one ligand to this protein ensemble using RosettaLigand.
Thanks in advance.
Dear Rosetta Users,
I am trying to generate 20000 structures by using RosettaLigand, but the application keeps on crashing with the following errors:
[ ERROR ] UtilityExitException
I am attempting a ligand docking run in a P450 docking both the heme cofactor and ligand simultaneously. I was able to have a successful run with just the heme group but when I attempt to add in the ligand I get an error. Currently, I've been getting the error "unrecognized mm_atom_type_name W" where W is the chain name for my ligand. I've attached my docking file, initial structure pdb file, and my options file so they can be looked at to help me resolve this issue. Thanks in advance!
I am facing trouble running the script ligand interface.py. I have prepared the pdb file and params file as instructed. I have also added the params file to the default directory and updated residue_types.txt file. The following error gets invoked. Please do help rectify the error.
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