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fix the left part doesn't work

Submitted by albumns on Wed, 2012-11-07 00:02

hello:

I am using the following protocol which someone used in the forum to build loop based on crystal structure. I am going to fix the left part of the region since they are from crystal structure and I find that all the regions are rebuild by Rosetta. I am just wondering, where is the problem?

thank you very much

/opt/rosetta3.4/rosetta_source/bin/loopmodel.default.linuxgccrelease \
-database /opt/rosetta3.4/rosetta_database \
-nstruct $nstruct \
-loops:input_pdb ../crystal.pdb \
-loops:loop_file ../input.loop \
-loops:remodel perturb_kic \
-loops:refine refine_kic \

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Rosetta 3 - Applications

rosetta compilation error

Submitted by jarek on Tue, 2012-11-06 04:05

I am trying to build rosetta on a cluster that is running SUSE 2.6.16
I use scons supplied with the rosetta 3.4 package.
In rosetta_source I run this command: external/scons-local/scons.py bin mode=release

At first everything seems to be working, it keeps on compiling for 1 hour and then I get the message below.
Any idea what could have gone wrong ?

Jarek

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Rosetta 3 - Build/Install

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

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