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Units of kT for MC mover

Submitted by msellers on Fri, 2010-12-10 05:40

Hello, I'm wondering how we can connect the values for kT specified for an MC mover, to a real world temperature and Boltzmann's constant. As per this post:
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Tue, 07/07/2009 - 10:37
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smlewis
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Rosetta reports energies in Rosetta Energy Units.

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PyRosetta - General

Fold tree not correct for multi-chain partners

Submitted by msellers on Fri, 2010-12-10 05:35

I have a two partner docking problem, where the first partner is made up of chains A,B,C,and D, and the second partner is chain X. They are loaded from a single PDB.

In my script I am using:

dock_prot = DockingProtocol()
dock_prot.setup_foldtree(p,'ABCD_X')
print p.fold_tree()

Which prints:

FOLD_TREE EDGE 1 117 -1 EDGE 117 118 1 EDGE 118 227 -1 EDGE 227 235 -1 EDGE 227 479 4 EDGE 235 236 2 EDGE 236 353 -1 EDGE 353 354 3 EDGE 354 471 -1 EDGE 479 472 -1 EDGE 479 486 -1

However, once the pose is created, a command such as:

p.pdb_info().pdb2pose('X',1)

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PyRosetta - General

Interface Design

Submitted by brettth on Wed, 2010-12-08 07:25

I am using Rosetta to help design a protein to bind to another protein. Basically, I am taking a known protein/protein interaction, changing some of the residues on one partner, and then asking Rosetta to make compensatory changes on the other partner so that they still bind. Currently, I am basically creating a PackRotamersMover object, allowing the interface residues on the designable protein to be any AA, and then outputting a number of decoys, and examining the lowest scored decoys.

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PyRosetta - General

"Unhandled exception" error while running on Windows

Submitted by EricD on Tue, 2010-12-07 13:43

Hello,

I have successfully installed Rosetta3.1 on Windows 7 (64-bit) using Visual C++ 2005. I am trying to perform de novo structure determination.

Every time I try to run -prna, I am stopped halfway through and given the following error:
"Unhandled exception at 0x004e2a6f in rosetta++.vc.release.exe: oxC0000094: Integer divison by zero."

Google searching suggested I perform a reinstall, but I've tried and received the same error. I have very limited programming knowledge, so this error means nothing to me. Any help will be appreciated!

Thanks!

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Rosetta++ - Build/Install

Specifying disulfide bonds

Submitted by msellers on Thu, 2010-12-02 10:38

I am finding that my structures generated with VMD containing disulfide bonds are not being preserved when used in PyRosetta. The sulfur atoms in the initial PDB are ~2.05 ang apart, but after a docking run they are as far as 11 ang. It seems that Rosetta automagically calculates disulfide energies--I am seeing non-zero values for "dslf_ss_*" in the .fasc output from docking, so I'm just wondering if there is something else I need to do.

Thanks.

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PyRosetta - General

high resolution protein docking doesn't work

Submitted by albumns on Thu, 2010-12-02 02:36

Hi
I am using rosetta docking_protocol.linuxiccrelease @flags > docking.log for initial protein docking. 10000 initial pose(only backbone) were generated by this. Then I clustered top200 pose by cluster.linuxiccrelease @flags >& cluster.log &
The best scoring one from the largest cluster were submitted for rosetta refinement(add sidechain and hydrogens) :relax.linuxgccrelease @flags > log

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Rosetta 3 - General

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