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Symmetric local protein docking

Submitted by efratmas on Tue, 2011-01-11 03:00

Hi.
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:

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Rosetta 3 - General

error about 'std::bad_alloc' during running

Submitted by zhisheng on Mon, 2011-01-10 09:45

Hi,

I just installed rosetta and used a small peptide to see whether rosetta worked properly. But when I run runRosetta3.com 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
Aborted

How to fix this problem?

Many thanks!

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Rosetta 3 - General

why not scoring function in loop model?

Submitted by albumns on Thu, 2011-01-06 00:13

Dear:
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
-loops
-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
-build_initial
-remodel quick_ccd
#-refine refine_ccd

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Rosetta 3 - General

how to cluster loop?

Submitted by albumns on Wed, 2011-01-05 19:48

Dear:
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?

THX

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Rosetta 3 - General

where do new .params files go?

Submitted by einew on Wed, 2011-01-05 12:09

I used molfile_to_params.py 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?

Thanks!

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Rosetta 3 - General

first try at relaxing a structure

Submitted by einew on Wed, 2011-01-05 11:09

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:
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 1 in file 8cp0
apo.pdb. Best match rsd_type: LEU_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 2 in file 8cp0
apo.pdb. Best match rsd_type: TYR
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 3 in file 8cp0
apo.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 4 in file 8cp0

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Rosetta 3 - General

Segmentation fault when reading VMD PDB

Submitted by msellers on Mon, 2011-01-03 07:14

All,

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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PyRosetta - General

does rosetta good at peptide-protein docking?

Submitted by albumns on Mon, 2010-12-27 18:51

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?

THX

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