Hi all,
I performed antibody-antigen docking experiments following the Rosetta antibody-antigen docking protocols. For each antibody-antigen pair, I compared the interface scores (I_sc) among the different antigens with small difference in sequence.
Dear all,
I'm really struggeling to repeat the published procedures to run ReplicaDock2.0 (Local and Global), let alone adopt it to my needs.
Hello,
I have been running this command other pdbs:
python2.7 /mnt/c/Users/No\ LOL/Desktop/Rosetta-jgustat/rosetta_bin_linux_2020.08.61146_bundle/main/tools/protein_tools/scripts/pdb_renumber.py \--norestart HER2_C_G3_A_full.pdb HER2_C_G3_A_full.pdb
and it has worked. Yet when I run it for my current pdb, it produces this error:
Greetings,
I'm trying to perform an Ensemble Docking using RosettaDock 4.0 as the protocol. The structures were relaxed, and ensembles generated for both proteins. Once the runs start using the MPI version:
$ mpirun -np 24 --hostfile $PBS_NODEFILE docking_protocol.mpi.linuxgccrelease -in:file:s ../input/4udt_AB_prepack.pdb -in:file:native ../input/4udt_xtal.pdb -unboundrot ../input/4UDT_AB_renum_noHET.pdb -nstruct 5000 -ensemble1 ensemble/4udt_A_ensemblelist -ensemble2 ensemble/4udt_B_ensemblelist -partners A_B @dock_ensemble_flags
Hi every one
I have encountered with an error "Your GitHub account does not have verified academic email address" while my email address damain is @mazums.ac.ir which is for Mazandaran university of medical sciences in Irna (https://en.mazums.ac.ir/). would you please help me.
cheers
Hello,
I was performing various ligand docking procedures using Rosie and when I was analyzing the data I noticed that some decoys had multiple entries in the score file with different scores but the same decoy model name. Is this normal and if so how can I interpret it?
For example one of my procedures created 200 docking models but the score file had 204 entries, 4 of which referenced already referenced models.
Thank you!
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).
Hello everyone,
I recently read in the manual that "partners" parameter must be set in the order of how they are set in the PDB. However, I was unaware of this previously and set my partners as LH_A, while my pdb files are ordered as HLA. The docking is working and has been running for a couple days, but I am wondering if this will affect the results of the docking?
