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error mesages from RosettaDock

I am using RosettaDock (from Rosetta 3.1 package) to generate some predicted protein complexes. I got some errors during a few cases in my dataset.

It says
"ERROR: f.check_fold_tree()
ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 327".

I also attached a log file of one of these error cases.

Could some one help me to solve this problem? Thanks a lot.

Alan

Post Situation: 

low resolution blind protein-protein docking with a ligand

We're trying to repeat published docking results with Cytochrome C & Human neuroglobin, because we want to compare that to docking a different globin to Cyt C. Low resolution blind docking of the protein only [no heme groups] produces 1000 structures 2-3 days on the linux station we're using. However, the interface region in the published structure includes the space in which the hemes sit, so we think including the hemes will be more accurate. With the help of kind people on this forum, we were able to get to the requisite params files & docking partner syntax.

Post Situation: 

Structure prediction based on template -> Documentation comparative modeling of protein structures

Dear Forum,

I am playing around with Rosetta since 2 days now but I still can't get a good output. So here is what I am doing. First to proof the efficiency I try to predict the structure of an amino acid sequence from which the crystal structure is already determined by using this command:

Post Situation: 

I am a beginner in rosetta software and need help to build params file

I am a beginner in Rosetta. I would like to use match to define a binding site with constraints. But my ligand that I want to define is a metal. So I define my metal in a pdb file as:
HETATM 3835 FE HEM 1 17.140 3.115 15.066 1.00 14.14 FE3+
END

Then I create the .mol file by using avogrado software and I compile in rosetta by using molfile_to_params.py
But it isnot working. So I compil the demo that rosetta propose and it is ok. Apparently the problem is my ligand because in the .mol file I have only one line.

Post Situation: 

a trouble during floppytail modeling

Hello,
I am using FloppyTail in Rosetta 3.2. After the first stage, the centroid modelling, there was really an expected folding in my designated tail region. However, my problem was that the protein containing floppy tail dissociated from original protein complex significantly, but the other components were still well organized as previous. Also, the second stage, fullatom modeling, could not correct it. How could I deal with it?
I thought those input start and stop residues positions were right, fragment file was also provided.

Thanks very much.

Post Situation: 

Re: Basic python scripts for File Manipulation

Hi,

I am searching for the following files :-

File Manipulation

cat_silent.pl: concatenate silentfiles
changeChain.pl: change the chain id of a PDB
compose_score_silent.py: generate a silentfile from a set of PDBs
createLoop.pl: create a dummy structure from a sequence of amino acids
createTemplate.pl: create a homology model template from a FASTA file and a homologous structure
make_coords_file.py: generate .coords format from native pdb (for input to cluster_info_silent.out, see below)

Post Situation: 

rosetta 3.1 recognizes PO4 group in dockinglocalrefine option?

Hi,
I have been trying to dock 2 peptides together, one of them phosphorylated at the serine. It seems that only the docking_local_refine option recognizes the phosphorylated group and generates an output. From what I understand, this option is used only when biological relevant information is available for the interaction interface. In the case where it is absent, is there other ways for the other docking options to work?

Greatly appreciate any help in this! =)

Post Situation: 

Ab Initio Modelling of Protein with Small-Molecule Cofactor

Hello everyone,

I am in need of some help regarding the ab initio folding of a protein in the presence of its cofactor. I already made myself familiar with the tutorial that comes with Rosetta where you have that Zn-ion binding to a small peptide. Still I don't have any clue how to setup an ab-initio-relax with a small molecule.

The actual situation is the following:
The cofactor is FAD.
I know which residues of the protein are most likely to be involved in binding of FAD.

Post Situation: 

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