for example:
https://rosie.graylab.jhu.edu/snug_dock/viewjob/75063
When those jobs could be finish?
Thanks a lot
Hello, I am trying to do protein design using a protocol derived from RosettaLigand ligand docking.
When I run Rosetta Design as the following command line, everything seems correct and there are output structures (pdb files). The problem is that it takes ages to get the results. In average, it will take 15~20 mins to get one models. For 1000 models, it spent 9 days. I think there is something wrong, but I don't know how to solve it.
Hi, everyone ! I try to extract the docking pose from a silent file which contains the ligand docking results. Here is my code:
extract_pdbs.mpi.linuxgccrelease -in:file:silent job01.o -in:file:tags BLS_0092 -extra_res_fa BLS.params -in::file::fullatom -database main/database
and the followings are output warning info:
Hello,
I'm trying to use rosetta mpi to dock a library of molecules, but I got this error:
mpirun noticed that process rank 1 with PID 26757 on node c1117 exited on signal 6 (Aborted). It seems there is an error in one node and then causes the whole job aborted, so I wonder if there are any parameters to skip the molecules with problems and continue docking. Many thanks !
Best,
Ruska
There is a flag that I cannot recall that stops Rosetta from using ligand params from PDB and instead use the one from n:file:extra_res_fa and n:file:extra_res_cen.
What is it? I cannot find it in my notes and in the documentation.
I am new to Rosetta and was trying Protein-Protein Docking tutorial. I was about to run a local docking but it gives me an error saying that
"ERROR: Cannot open file "input_files/col_complex.pdb"
so when I checked the "flag_local_docking" file there is a file called col_complex.pdb needed as input. But I don't understand how to build this file.
Hi:
In the docking results. Is RMSD have something to say for docking affinity?
Thanks a lot
Jess
HI,
I have PDB strucures of antigen- antibody complexs. want to studythe hydrogen bond pattern at the ineterface and also the shape complimentarity. As per the following manuscript (Kuroda et al, (2016) Bioinformatics, 32(16):2451-2456) the command line
report_hbonds_for _plugin.linuxgccrelease
-s
-prevent packing true
sc.linuxgccrelease
hi
I am docking an antibody to antigen using the snugdock server. Just wanted to know whtat is the reference structure in the the RMSD deviation in the score.sf files. Is it the structure with the lowest rosetta energy. In case if you want to compare the original structure of complex with decoy structure what is the easiest option. i am attaching the gnuplot out put of the Total Score Vs RMSD . Any help would highly be appreciated
Dr. Suji george
