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Docking

jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease

Category: 
Docking

Dear Rosetta community,

I am looking for a reason why my simulations stop before -nstruct is reached. This happens when I use rosettascripts.mpi.linuxgccrelease for some flexible docking. As many decoys don’t pass the Rosetta filters, I set -ntrials to 100.

And then, with:

-nstruct 500

-ntrials 100

I get exactly 500 decoys (which I anticipate), but for:

-nstruct 30 000

-ntrials 100

Post Situation: 

Method to keep ATP in the certain position in the prepack step

Category: 
Docking

Dear all,

during I'm using flexpepedock, I gengerated a param file for the ATP. But in the prepack step, the program moved my ATP out of the ATP pocket. I've used movemap and constraint file but it didn't work. The ATP still got "kick out".

I was wondering how to let ATP not move during the prepack step?

I attached the PDBs before and after prepack step as well as my prepack flags.

Thank you!

Post Situation: 

how to fix the ATP HETATM by using movemap or constraint file?

Category: 
Docking

Dear all,

I'm doing docking peptides to kinase structure by using flexpepdock. In the meanwhile I need ATP in the kinase structure, therefore I generated a param file for ATP. But after the prepack mode, the ATP has been removed from the pocket to the somewhere in the structure. Here is my question:

1) how should I fix the ATP in the pocket without any movement? Movemap or constrain file?

2)I was told to use movemap to fix the ATP. But I don't know how's the rosetta numbering of the HETATM. 

Post Situation: 

PlaceStub filter

Category: 
Docking

Hi everyone

Using placestub application, I want to place a set of stubs in target protein to use them for protein binder design. In this way, I want use 1000 scaffold (proteins to be substituted by appropriate stubs). Everything is OK with producing stubs, inverse rotamers, docking. But when I run placestub xml, it gives me this type of error in last line:

 

Post Situation: 

How to extract antibody from a set of pdb file may may contain antigen?

Category: 
Docking

Dear all,

I have a set of pdb structure files that contain antibodies but may or may not contain antigens. I want to extract only the antibodies from each of these structures. Do anyone know how to do it?

Best regards,

Yeping Sun 

Post Situation: 

keep ATP in the kinase-peptide structure while docking

Category: 
Docking

Hi,

i'm trying to dock a peptide into kinase. It's very important to keep ATP molecule in the kinase ortherwise some peptide simulation model will occupy ATP's position.

But the flexpepdock will remove all not aminoacid molecules. I was wondering is there any way I can do that ? Or an alternative module on Rosetta? 

Thank you!

Post Situation: 

Error: Could not find scorefxns and name score12 in Datamap in rosetta_bin_linux_2017.39.59729_bundle

Category: 
Docking

Hi everyone,

I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:; 

 

 ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol  docking_stubs.xml

 

Post Situation: 

How to make a resfile

Category: 
Docking

Hello,

I am new to using Rosetta. I would like to make a res file to mutate through all 20 amino acids in a Protein-protein interface and predict binding energy using RosettaDesign.  This might be a stupid question but how to you make a resfile? Do you write it in text edit? Is the file extention .res?

I have found the refile syntax page from Rosettas website but it does not say where you type any of the commands into or how to save it.

Post Situation: 

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