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Error in snugdock application

Submitted by syntekabio2019 on Tue, 2024-05-28 00:59
Category: 
Docking

 

 Hi all

 Recently  I;m involved in antibody related project

 While I'm running snugdock application with my antibody( H chain: Lchain) and antigen complex

 I got following error :

 Can't find residue type 'VRT' in type set of mode fa_standard

 In my PDB , only standard amino acid residues are there.

 and I think VRT means something like virtual related object.

 I don't know why this kind of error occur

 Attached file is my pdb file with this error

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Rosetta 3 - Applications

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

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