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FastRelax results in bad structure

Category: 
Structure prediction

I use FastRelax to do refinement for my pose. However, the structure becomes completely different and of bad quality after refinement. Is there something wrong with my relax file?  If not, why did this happen? I added the original  and refined pdb file.

The relax file is below:

switch:torsion
repeat 2
ramp_repack_min 0.02  0.01     1.0 100
ramp_repack_min 0.250 0.01     0.5 100
ramp_repack_min 0.550 0.01     0.1 100
ramp_repack_min 1     0.00001  0.1 100
accept_to_best
endrepeat

Post Situation: 

Clustering problem

Category: 
Scoring

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

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Post Situation: 

multi ligand docking using rosetta script

Category: 
Docking

 

  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

Category: 
Compilation

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.

Best,

 

Post Situation: 

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