You are here

Docking

Run protein-protein docking parallelly by mpi

Category: 
Docking

I run docking_protocol parallelly by mpi (Command: mpiexec -np 10 $ROSETTA_BIN/docking_protocol.mpi.linuxclangrelease @flag_docking).

But the error below occurred.

[ERROR]

-----------------------------------------------------------------------------

Primary job terminated normally, but 1 process returned.

a non-zero exit code. Per user-direction, the job has been aborted.

Post Situation: 

snugdock(sequence position requested was greater than the number of residues in the pose)

Category: 
Docking

Dear users, 

When I did snugdock, my native input structure and snug input structure share the same number of residues and residue indexes, but the error still shows up "sequence position requested was greater than the number of residues in the pose".
I attach both files and appreciate any suggestion. Thanks!

Post Situation: 

Prepacking crashing using metalloprotein

Category: 
Docking

Good evening, 

I'm trying to run an ensemble protein-protein docking to a protein containing a metal cluster (2Fe2S). I was able to generate ensembles for both structures, but at the Prepcking stage the application just crash. Here is the command:

$ docking_prepack_protocol.default.linuxgccrelease -in:file:s ../input/mnt_bcl2_relaxed.pdb -ensemble1 ../ensemble/mnt/mnt_A_ensemblelist -ensemble2 ../ensemble/bcl2/bcl2_B_ensemblelist -partners A_B -in:auto_setup_metals true @prepack_flag

Here is the error message:

Post Situation: 

Help to understand docking results

Category: 
Docking

Dear colleagues, everything's ok?

I have done a docking experiments between enzyme and inhibitor.

I did global docking on cluspro web serve, following did a local and refine docking procedure.

Wight parameters, I should look to compare the docking results with my kinetics data

total score X rms; I_sc X Irms or something else?

I ask for help because some results appear so artificial.

Thanks any way

Ricardo

 

Post Situation: 

Pages

Subscribe to RSS - Docking