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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

DockingProtocol().set_autofoldtree Question

Submitted by brspurri on Fri, 2011-06-03 08:07

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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PyRosetta - Scripts

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

Using D-amino acids in Rosetta docking

Submitted by moehle on Wed, 2011-06-01 00:49

Hi,

I have tried to use the docking protocol of Rosetta3.2.1 for docking of well structured peptide to protein receptor. The peptide contains the D-amino acids(D-Pro, D-Arg). The corresponding "params" files are located in "residue_types/d-caa"

First I changed the related lines in "residue_types.txt", to get the params files active. The residue types seem to be recognized by Rosetta but it fails with the following error message

ERROR: unknown atom_name: DPR H
ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1454

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Rosetta 3 - General

installation using scons on cygwin

Submitted by isengupta13 on Tue, 2011-05-31 11:50

Hi
I have been trying to install rosetta v2.3 on my laptop which has the windows xp operating system. I have installed cygwin as well as scons. When I type scons mode=release in the rosetta++ directory I get the following error:

scons: Reading SConscript files ...

scons: warning: The Options class is deprecated; use the Variables class instead.
File "/usr/local/rosetta/rosetta++/tools/build/setup.py", line 32, in setup_build_options

scons: warning: The EnumOption() function is deprecated; use the EnumVariable() function instead.

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Rosetta++ - Build/Install

protein structure prediction using relax -- high-powered jobs

Submitted by rfieldhouse on Mon, 2011-05-30 18:29

Quick question, I am interested in refining a few homology models with long runs of the relax protocol. I find the run time is fairly short on my local supercomputer system, and I'd like to make maximum use of the resources available to me. So, how do I improve my models by refining for a week instead of just a few minutes without having the job exiting? (Note: I believe the run exits normally.)

Also, is there a good order to use the applications when it comes to relax / loop modeling / backrub?

Thanks,

Rob

***

My command:

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Rosetta 3 - Applications

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