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Missing common atom definitions in constraints

Submitted by ic3reyes on Sat, 2011-06-11 13:09

Hi all,

I'm using CS-Rosetta and trying to input a constraint file for specifying backbone NOE's. Rosetta 3.2 works great for dNN constraints, but for some reason it's not recognizing HA atoms. Here's an example couple of lines from my inputNOE.cst file:

AtomPair H 33 H 50 BOUNDED 1.80 5.25 0.50 NOE ;dist 5.000 1.800
AtomPair H 44 HA 38 BOUNDED 1.80 5.25 0.50 NOE ;dist 5.000 1.800

The first line and all of it's kind with "AtomPair H res# H res# ..." works fine. When I try and run my file with dHAN constraints formatted like in the second line, I get:

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Rosetta 3 - Applications

Is it possible to use two broker files

Submitted by kalabharath on Wed, 2011-06-08 01:01

Hi friends

as a part of a project I am using rosetta to predict structure from nmr data. It currently uses a broker file flag to pass the input data. I am wondering is it possible to supply two broker files and use the data from both the files . Currently when i do that the second parameters are overwritten with the first one.

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Rosetta 3 - General

How to input pdb to rosetta format add "missing" residues to pdb file

Submitted by zhisheng on Tue, 2011-06-07 09:51

I got a structure from CS-Rosetta and want to refine it with rosetta. In the protocol it says

1. Input pdb files into Rosetta format
2. Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)
3. Idealize geometry

Does someone know how to do it in details? How to convert the format and add missing residues?

Many thanks

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Rosetta 3 - General

Why I have the different result with the same initial condition?

Submitted by mikelin on Sat, 2011-06-04 11:35

Dear all,

I use RosettaDock to find the binding site of the proteins. The structure is solved by NMR.
I use the default option:
docking_protocol.mpi.linuxrelease -database
in:files:s vegf_vegf.pdb -docking:randomize1 -out:nstruct 1000 -out:file:o vegfdimer

I did twice with the same option and the same pdb file, but the result is different.
The first one is right. The second is wrong. I don’t know what is the reason?
It seem that it is not reproducible.

I search the forum to fine some answers.
1. NO other data: lowest score = best result

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Rosetta 3 - General

ResidueDecompositionCalculator.cc:155: internal compiler error: Segmentation fault

Submitted by pietro1968 on Thu, 2011-06-02 09:31

Hello everyone,

I am trying to install Rosetta 3.2.1 on my x86_64 GNU/Linux machine,
running the 2.6.31-14-generic kernel #48-Ubuntu x86_64 GNU/Linux

I run Python 2.6.4

The compilation fails, below is the bottom of the log, please suggest what to do.
Is there an easy way of switching to another freely available c++ compiler for example, and how would I do so?

Thanks for any piece of advice you'll be able to provide!

Pietro

PS I attach a larger chunk of the logfile

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Rosetta 3 - Build/Install

Native gives higher (positive) than lowest energy and clustered decoys

Submitted by tiagogomes89 on Thu, 2011-06-02 07:19

Hi,

My native structure gives higher (positive) energy than lowest energy and clustered decoys (170 vs -77) with an output of 40000 decoys using abnitiorelax app.
The protein is an all beta-sheet and small (40 aa). From papers i`ve read and looking at the hydrogen bond terms at the rosetta energy function, i know it isn`t very good
at modeling this kind of proteins. I`m going to try it anyway. Any ideas why this happens? What am i doing wrong?

Thanks for the help,

Tiago

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Rosetta 3 - General

Anyone here knows what is the protocol capture archive???????!!

Submitted by MajorID on Thu, 2011-06-02 01:50

Hi,
I'm learning FlexPepDocking from the following paper:

"Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors"
And I want to see the scripts the anthor used, which is named 'FlexPepDockAbInitio' in 'protocol capture archive'.
What is the "protocol capture archive"?! I've googled but found no useful result..
Best,
Yuan

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Rosetta 3 - General

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