The problem hasn't been solved
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:
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.
Could anyone tell me how to model the structural change of one specific residue with phosphorylation? Thank you very much.
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.
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)
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! =)
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.
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:
Where can I find information that explains what the score values are and how to interpret and compare them? I'm new to Rosetta and still trying to learn what is going on while I learn how to run the program; so excuse me if I missed something obvious. Also, is the primary source of information related to Rosetta in published papers or is there something more explanatory than the Rosetta manual? Thanks for any help.
Hi, I need some help here. I've been reading the document for fixbb protocol in this page: http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_...
In the box listing flags for rotamers, I found one called preserve_input_cb which is supposed to keep unidealized ca_cb bond parameters from input file. However, I cannot find which layers this flag belongs to. What's the key word should I put before the flag in the option file?