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Symmetric local protein docking

I installed Rosetta3.1 and I'm trying to use it for local docking of protein complexes witn Cn symmetry.
The program docking_protocol.linuxgccrelease is running and produces the results but it prints out a warning:
"core.scoring.SymmetricScoreFunction: Warning!!! Using a symmetric score function on a non-symmetric pose"

I'll be happy to know what am I doing wrong...

Here are my steps:
1) I have a model of a trimer that I want to refine.
I deleted one of the monomers and saved the remaining 2 monomers (chains A and B) in a pdb file.
2) I ran prepacking by:

Post Situation: 

error about 'std::bad_alloc' during running


I just installed rosetta and used a small peptide to see whether rosetta worked properly. But when I run in the 'rosetta' directory, it aborted at a 'Stage 4' sometime later. The following is the screen message,

Stage 4
Folding with score3 for 40000
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc

How to fix this problem?

Many thanks!

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why not scoring function in loop model?

I used the loop protocol to generate ab int loop and I found that there is no scoring information for the loop models and I don't know how to judge which one would be the best one. Could you please give me some advices? Here is my flag parameters:

-database /soft/rosetta3.1/rosetta_database
-input_pdb gbss.pdb
-loop_file gbss.loops
-frag_sizes 9 3 1
-frag_files /home/librahoo/Desktop/GBSS1_loop_refine/gb/aagbss109_05.200_v1_3 /home/librahoo/Desktop/GBSS1_loop_refine/gb/aagbss103_05.200_v1_3 none
-remodel quick_ccd
#-refine refine_ccd

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how to cluster loop?

I've build loop model based on Rosetta Loop protocol and I am going to cluster those loops based on cluster protocol. However, I found that the cluster protocol is designed for the whole protein and there is no option for clustering only a part of the protein.
So, I am wondering, is it possible only cluster a part of the protein?


Post Situation: 

where do new .params files go?

I used to create .params files for the two substrates for 'my' protein. I'd like to relax the modeled structure with these compounds present. I found that leaving these files in the current working directory wasn't right - relax still crashes because it doesn't recognize the residue. Copying the .params files into rosetta_database/chemical/residue_type_sets/fa_standard/residue_types wasn't right either, or wasn't enough. What else should I be doing?


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first try at relaxing a structure

I've just put up Rosetta, and am trying to run it for the first time. I get a lot of errors that look like this: [ WARNING ] discarding 1 atoms at position 1 in file 8cp0
apo.pdb. Best match rsd_type: LEU_p:NtermProteinFull [ WARNING ] discarding 1 atoms at position 2 in file 8cp0
apo.pdb. Best match rsd_type: TYR [ WARNING ] discarding 1 atoms at position 3 in file 8cp0
apo.pdb. Best match rsd_type: GLY [ WARNING ] discarding 1 atoms at position 4 in file 8cp0

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Segmentation fault when reading VMD PDB


I receive this output when trying to create a pose from a pdb file I outputted using VMD. Initially, it is giving me an error about "HSD" residues, which I rename to "HIS". Does anyone know what might trigger a segmentation fault at this particular location?

core.pack.pack_missing_sidechains: packing residue number 375 because of missing atom number 8 atom name CD1
core.pack.pack_missing_sidechains: packing residue number 377 because of missing atom number 8 atom name CD1

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does rosetta good at peptide-protein docking?

Generally speak the peptide docking is much more chalenged than protein-protein docking for the peptide backbone is much more flexible than protein. Because of this reason, many peptide docking tools would introduce annealing and solvent model. I am wondering, does Rosetta also good at such kind of work?

If I want to do a peptide docking, may I also use solvent model(such as TIP3 and so on) and annealing during the docking?


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