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Docking

script recommendations? for high res docking from low res

Category: 
Docking

Hi:

Is there a rosetta or pyrosetta script  (or general protocol) you would recommend for a pdb that already has a small molecule ligand docked in a low resolution docking model?

I used Zhang lab's BP Slim server to get this lo res docking, and now what I need to do is refine that model to high res, atomic scale.

 

thank you all so much, I am learning rapidly from this most generous and helpful community.  - Amy

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missing atom number 5 atom name CB

Category: 
Docking

I am contacting you because I am getting an error in results with Rosetta. Successfully finished protein-protein docking. I can see in the output that following lines complaining about missing atoms. I have prepared protein in ICM, Molsoft. I checked the input file those I have given as input.pdb, there were no missing any CB atoms in all amino acid. Docking finished successfully and generated score value. Do you think this missing atom will make any impact in score value? Let me know how can solve this problem. 

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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 *

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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.

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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

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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

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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.

 

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

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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 

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