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clustering PDBs from docking

Submitted by jbujons on Wed, 2024-04-24 08:34
Category: 
Docking

Hi,

I performed a protein-protein docking within rosetta by using a single receptor structure and several conformations of the same ligand protein. Now I am trying to cluster the results (aprox 1000 structures) using the cluster application included in rosetta by running:

cluster.linuxgccrelease -in:file:l pdblist -in::file::fullatom

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Rosetta 3 - General

Error in score funtion "hack_elec 0.42"

Submitted by intomybioverse on Sun, 2024-03-17 06:33
Category: 
Docking

Hello everyone!

I am getting this following error when I am trying to run a rosettaDNA application program in which i want to change the specificity of a protein so that it binds to a target DNA. In most published articles, I have seen "hack_elec 0.42 " or similar values. However, it's not working in my case. Can you help me with this?

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Rosetta 3 - Applications

several question in mpensemble dock

Submitted by lluoto on Tue, 2024-03-12 07:54
Category: 
Docking

Hey guys, I counterpart with problems as topic saying:

First, I want to use others computational results as reference to optimized docking option, so I have to relax them into same scorefunction, meanwhile relax the inputs which generate from different methods for better results and avoid disulfide bonds error due to different scorefunction, right?

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Rosetta 3 - Applications

Creation of crystal_complex.pdb for docking

Submitted by HBenson on Mon, 2024-03-11 08:57
Category: 
Docking

Hello all,

I have been trying to dock a library of ligands to a protein while following the Meiler lab tutorials. While I have been able to prepare most of the prerequisite files, I am unsure how I am supposed to obtain 'crystal_complex.pdb'. Trying to download the protein bound with a ligand .pdb file from the protein data bank and using that as my crystal_complex.pdb does not seem to work. While it seems that options.txt and dock.xml have been set up correctly, protein complex.pdb is the only thing preventing me from running the docking itself.

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Rosetta 3 - Applications

Stub Libraries for DockWithHotspotMover

Submitted by ayush_patel on Sat, 2024-03-09 22:43
Category: 
Docking

Hello!

I was a little bit confused about what exactly the stub libraries are and how we are supposed to generate them. From what I understand, they're simply just disembodied residues that we consider "important" to the interface in the docked complex. So, are the stub files just generated by taking a protein structure and deleting everything except for the hotspot residue, then saving that singular residue as a PDB file? Also, is it possible to assign hotspot residues to both chains that we are docking together?

Thank you so much.

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Rosetta 3 - Applications

Filters saying atom type does not exist on residue

Submitted by mdm95 on Mon, 2024-03-04 15:13
Category: 
Docking

Hi,

I'm currently try to dock a ligand into a dimeric structure using Rosettascripts. When I do normal docking everything goes okay but once I add filters it no longer functions, getting the warning  [ WARNING ] Residue 477 of type CHA does not have atom with type H4. The run will continue then fail at the end. This is the name for the atom in the PDB itself so I'm unsure what exactly is happening. I've attached the xml I'm using below, any help would be greatly appreciated! (Unfortunately the pdb was too large to attach.)

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Rosetta 3 - General

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