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model protein at low pH

Submitted by ytao on Mon, 2012-11-05 07:52

Hi,

I'm a noob in rosetta modelling. I need to model my protein at low pH, i.e. with protonated Asp and Glu residues. How should I setup the simulation(ab initio and relax)?

I found there are residue type files for fullatom protonated Asp and Glu in rosetta_source directory, but I don't know how to use them:(

Thank you very much,

Yisong

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Rosetta 3 - General

loop design

Submitted by varma on Sun, 2012-11-04 21:25

Hello all,
As a part of my work I have to redesign and exchange the loops of target protein with other loops (irrespective of the length) after going through some literature I have found that Fixed backbone design could help in redesigning the loops with desired residues but I couldn't find any method regarding loop exchange, Could any one tell me is there any reliable protocol to do loop exchange in Rosetta and also I would like to know whether my choice of fixed backbone design to redesign loops is a correct one. Please ignore my layman knowledge as I am new to Rosetta.

Thank you

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Rosetta 3 - General

mitochondria protein modeling

Submitted by rlwoltz on Fri, 2012-10-26 14:32

I am trying to model Opa3 which is a protein in the mitochondria. There is evidence showing that when this protein is mutated there is a build up of 3-methylglutaconic aciduria, type 3 (MGA-3). We are trying to find a ligand that is in the pathway of production/breakdown of this compound so we can mutate the amino acids the ligand would bind to. Because of the unique conditions in the mitochondria I don't really know where to start in predicting a stable model and a ligand binding site. Any suggestions or advice on what tools or programs to use?

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Rosetta 3 - General

Can't make NCAA's and D-aminoacids work

Submitted by jarek on Fri, 2012-10-26 09:10

Hi,

I'm trying to incorporate D-amino acids in some designs.
I followed the steps as in the recent thread on D-amino acids here:
http://www.rosettacommons.org/content/steps-use-d-amino-acids

1) I uncommented the aminoacids I need in residue_types.txt
2) I downloaded and unpacked the params files
3) I use the -score:weights mm_std in my docking protocol
4) I found the 3 letter codes in fa_standard/residue_types/d-caa and modified the input file accordingly.

When I run low resolution docking now, what I get is the following error message:

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Rosetta 3 - General

No output pdb files after docking protein and DNA/RNA

Submitted by yzq on Thu, 2012-10-25 08:23

I tried to dock the protein and DNA or RNA with perturbation flags, everything seems going well, but at the end of the docking, these is no output pdb files. Below is the information at the end of the log file, and also the flags are shown.

protocols.docking.DockingProtocol: Scoretype: interchain_contact score: 12, cutoff: 9.99
protocols.docking.DockingProtocol: Scoretype: interchain_vdw score: 0, cutoff: 1
protocols.jd2.FileSystemJobDistributor: Too many retries (max_retry_job = 10)
protocols.jd2.JobDistributor: 10MH_0001 reported failure and will retry

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Rosetta 3 - Applications

enzyme design and output_matchres_only

Submitted by petrikigor on Wed, 2012-10-24 18:45

I have successfully been able to run match, but enzdes remains elusive. Currently, I'm trying to figure out, if I used output_matchres_only in matcher (my PDB files only contain the ligand and catalytic residues), how do I load both the pdb file containing the scaffold and pdb files containing the matched site into enzyme design?

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