You are here

Docking

D100 Docking script error test.output

Category: 
Docking

Hi:  I have researched this error I am getting, but don't see any reference to it.   Thanks in advance for any help.

When I run

 

python D100_Docking.py --pdb_filename /81q1D100_Dock/ferudock81q1cds.clean.pdb --jobs 400 --job_output 81q1_docking_output --translation 3 --rotation 8 --PyMOLMover_ip off
 

I can't get past this error with the constant seed:

In [1]: import optparse

In [2]: from pyrosetta import *

Post Situation: 

Ligand Binding

Category: 
Docking

Dear Ligand binding Team,

I am writting this letter of appreciation to thank the team of Rosie Ligand Docking for making available such a powerful docking tool for researchers. We recently used the tool and got wonderful results using a difficult protein (oxidosqualene cyclase). We also want to thank you for making rarely available docking tool based on Induced-Fit freely available to academic users.

We hope that you continue providing the Rosie tools and keep updating the excellent Ligand Docking tool.

Post Situation: 

Highly negative total score

Category: 
Docking

I have performed a docking between a protein and a 15 residue peptide using flex pep dock. I have got a total score of around -1347, is this considered as good docking ? I am unable to predict whether the docking can be considered or not. Please help me. Thanks in advance:

The total score and other factors are as follows:

total_score

I_sc

Post Situation: 

Bound Ligand Protein-Protein Docking

Category: 
Docking

Hi,

I am trying to run on the Rosie server some docking2 tests with bound ligand in each protein. In fact, I would like to explore a situation of how two protein interacts with each other with bound ligand. However, when I launch jobs with ligand coordinates at its final site included in the PDB, the simulation fails and I receive an error message.

I, therefore, write to ask whether is it possible to do on ROSIE server?

I thank you all in advance,

Haresh

Post Situation: 

ERROR: Specified chain does not exist.

Category: 
Docking

Hello,

I am using already preinstalled software Rosetta 3.10 on ComputeCanada (CCDB). I have run demos tutorial of protein-protein docking, was running successfully. Later, I have submitted own protein-protein docking job. I got an error(see below). Please, I need to help solve this problem.

 

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

[ajanihar@gra-login3 input_files]$ rosetta_scripts.mpi.linuxiccrelease @docking_full.options -parser:protocol docking_full.xml -out:suffix _full -nstruct 5

Post Situation: 

Segmentation Fault

Category: 
Docking

Hi,

I am trying to use protein-protein docking with unbound ligand protein and, I still get this error(see below ). I would appreciate any suggestion or solution.

Looking forward to hearing from you.

Haresh 

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

Post Situation: 

Does Snugdock remodeling of H3 loops include the kink constraint as in RosettaAntibody?

Category: 
Structure prediction
Docking

I am docking an antibody that has 20 residues in the H3 loop.  I realize that this is a very challenging case.  From the 2017 paper by Weitzner and Gray, I understand the importance of a kink constraint in H3 loop modeling.  I want to know if the H3 loop remodeling that occurs during snugdock includes the kink constraint.  If not, I am concerned that the kink will be lost during remodeling, especially for this long loop.

 

 

Post Situation: 

help surface_docking peptide on ice

Category: 
Docking

Hello everyone,

I am trying to use Rosetta surface_docking protocol to dock a 12 residues peptide on an ice slab.

I tried different formatting options of the input ice - peptide PDB file, but the software crashes.

After looking at the existing (Unsolved) posts on the forum, I created a PDB file formatted in this way:

Post Situation: 

Pages

Subscribe to RSS - Docking