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Clustering problem


Hi guys.

I met a problem when I was doing the clustering. I excuted this command but it was unexpectedly ended killed and had no result. I've 200 pdb files in this folder.

I'll be really grateful if it can be solved.

$ /home/suuo/Rosetta/main/source/bin/cluster.default.linuxgccrelease -database /home/suuo/Rosetta/main/database -in:file:fullatom -cluster:radius 3 -nooutput -out:file:silent ./cluster.out in:file:s *.pdb




Post Situation: 

multi ligand docking using rosetta script



  Hi all.

  I'm trying to dock  my ligand with HEM to CYP using rosetta script with XML protocol

  overall running process seems to complete without any problem, and rosetta script seems to recognize HEM and  ligand as separate entity

  But in some conformer generated by rosetta-script, there is severe clash between HEM and ligand.

  For this kind of conformer, rosetta total_score was extremely high and I could filter out this kind of unfavorable structure based on rosetta score

Post Situation: 

opencl support programs


Hi, All:

        We just compiled opencl version of rosetta. But when I run rosetta_scripts.opencl.linuxgccrelease, there is no running processes found in GPU. I am just wondering if GPU is supported after opencl version is successfully compiled. Thanks.



Post Situation: 

GeneralizedKIC loop closure error

Loop Modeling

Dear Rosetta Community,

I am trying to generate conformations for a 29 residue cyclic peptide with N-C terminal cyclisation. I've written a Rosetta Script that declares a bond between the N and C terminals and then performs a loop closure based on GeneralizedKIC.

However I am facing the following error:

Post Situation: 

Pyrosetta score protein structures with missing atoms in sidechain


I have a question regarding Pyrosetta. Currently, I want to use pyrosetta to score some protein structures but with missing atoms in sidechain. So my protein structures contrain full-atoms for backbone but missing one or two atoms per residue on sidechain. I used pose_from_pdb to read my protein structure (pdb). But it seems pysoretta will fill in the missing atoms according to rotamer library. Is there a way to prevent it so I can just score my structures with missing atoms on sidechains?  

Thanks a lot for the help,

Post Situation: 


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