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Dunbrack rotamer energy term...

This question is regarding the implementation of the Dunbrack rotamer energy term (fa_dun).

Based on my understanding of the implementation in Rosetta 2.3, I noticed that the fa_dun energy is comprised of two components:
1) A backbone-dependent probability of the rotamer : E = -log (p)
2) An "un-normalized" gaussian penalty parametrized using the average chi angles and the standard deviations for the rotamer: E_penalty = -log (gaussian)

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FlexPepDocking with GDP-bound protein

I have a problem when doing the FlexPepDocking to a receptor with GDP bound, but it stop with an error, saying that GDP is an unrecognized residue. When I add a flag "-remember_unrecognized_res", it goes well but GDP was still missing in the output structure. I believe GDP is involved in the binding and I don't want to ingore it in the docking. And I check the database, GDP.params is in /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/nucleic.

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Missing common atom definitions in constraints

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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Is it possible to use two broker files

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

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

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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DockingProtocol().set_autofoldtree Question

I'm at a loss of how to switch DockingProtocol().setup_foldtree to DockingProtocol().set_autofoldtree in the DDG script. A simple substitution clearly doesn't work; stating that it does not match the C++ signature.
Can someone post how to overcome this?
Many thanks,
Brett

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

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

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

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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