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low resolution blind protein-protein docking with a ligand

Submitted by einew on Sun, 2011-03-20 13:59

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.

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Rosetta 3 - General

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

Submitted by maxebert on Sun, 2011-03-20 01:15

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:

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Rosetta 3 - General

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

Submitted by nais on Fri, 2011-03-18 13:37

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.

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Rosetta 3 - General

a trouble during floppytail modeling

Submitted by chenchaozhao on Tue, 2011-03-15 03:59

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.

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Rosetta 3 - Applications

Re: Basic python scripts for File Manipulation

Submitted by bharat_46010 on Mon, 2011-03-14 19:44

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)

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Rosetta 3 - General

rosetta 3.1 recognizes PO4 group in dockinglocalrefine option?

Submitted by nilkoeg on Thu, 2011-03-10 23:19

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! =)

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Rosetta 3 - General

Ab Initio Modelling of Protein with Small-Molecule Cofactor

Submitted by jurkm on Thu, 2011-03-10 06:56

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.

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Rosetta 3 - General

Rosetta3.2 cluster application file-reading error

Submitted by mdyini on Wed, 2011-03-09 16:59

Hi, I was trying both Rosetta3.1 and Rosetta3.2 to do clustering. I had normal result from Rosetta3.1. But Rosetta3.2 failed to work. I used the same data set (generated by Rosetta2.3.0 abrelax mode), option and command, and the path is correct. I also got the error messege:

ERROR: Illegal attempt to score with non-identical atom set between pose and etable
ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 80

And in the log file, it says:

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