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Symmetry Docking and Clustering with Ligands

Submitted by skovacs on Wed, 2012-03-07 16:46

Greetings Rosetta Team,

Now that I've resolved my ligand_docking issues (big thanks to Rocco!) I would like to generate and screen symmetric protein+ligand homo-multimer structures.

First, in order to get SymDock to recognize my ligand and generate output, I had to rename one of the ligand's carbon atoms "CA".
Not a big deal, but it required changing the name for each occurrence of the ligand (input .pdb, parameter files, and rotamer libraries).

For the test case, SymDock.linuxgccrelease was run using PBS on four cores with the following flags:

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Rosetta 3 - Applications

redesign a enzyme by fixing the active site

Submitted by Lindsay on Wed, 2012-03-07 08:23

I want to design the sequences of an enzyme. I am not sure which method should I use. I am thinking of 2 methods:
1. Use fixbb and fix the enzyme site of the protein. just design the other part of the protein
2. Use Enzyme Design of rosetta 3.3. But this program seems only design the active sites.

Do you have any ideas? Thank you very much!

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Rosetta 3 - General

Fix back bone design fixbb

Submitted by Lindsay on Tue, 2012-03-06 12:30

Hi,
I use Rosett_3.3 to design a protein whose length is 166. And the command is
fixbb.linuxgccrelease -s protein.pdb -resfile protein.resfile -ex1 -ex2 -nstruct 1 -database $ROSETTA_DATABASE -jran 111111 -fast_sc_moves True

However, it takes me more than 2 hour to finish the job. I use rosetta 2.3 to design the same protein with the same parameter. It takes me only 1-2 minutes.

Could you please tell me what parameters should I use to make the program fast?

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Rosetta 3 - General

getting Rosetta to work with Phenix

Submitted by satyshur on Sun, 2012-03-04 12:54

I am trying to get Rosetta to work with Phenix phenix-1.7.3-928. But first I need to
get rosetta compiled. It does not compile without an error.I start with:

[rosetta@paprika ~/Desktop]$ python -V
Python 2.6.6

python scons.py bin mode=release

and it runs for a while and then:

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Rosetta 3 - Build/Install

is it possible to generate models without hydrogen?

Submitted by albumns on Fri, 2012-03-02 12:24

I am using the kinetic loop refinement protocol these days. Since my protein is large than 300aa and the loop is over 20 aa. So it is really time comsuming even I use 24 CPU to run the jobs. It only generate 1 model after one hour.... I am planning to generate 5000 loop models. Is it possible to generate the loop model with hydrogen? At least without hydrogen for the no loop region?

THX

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Rosetta 3 - General

a question about loop refinement

Submitted by albumns on Fri, 2012-03-02 09:38

Hello:
I've got a crystal structure and there is a loop region which contains 20 aa was missed. I am planning to fill in such loop by Rosetta. However, I found that there are three different methods for loop refinement in Roseeta:

Loop Modeling
Fragments Based Loop Modeling
Kinematic Loop Modeling

Do you have any idea which one is better for my case?I've complied Rosetta by command:

scons bin mode=release extra=mpi

I don't whether those refinement can be supported by mpi multiple thread.

Thank you very much
best

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Rosetta 3 - General

FloppyTail bugs for N-terminal tails

Submitted by Dave C on Thu, 2012-03-01 13:06

Hi all. Recently I've been using the FloppyTail application to try and model the N-terminal floppy region of my protein. I ran into (and solved) two issues, one that I'm sure is a genuine bug, and another that may be known but is nonetheless very serious. I am running rosetta 3.3 on a machine running MacOS server 10.5. All tests used the '-C_root' option, and had my protein listed first in the pdb.

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Rosetta 3 - Applications

ddG Monomer Low Res Protocol Convergence

Submitted by harshkhare on Thu, 2012-03-01 00:45

Dear Developers,

First question!! :-

I am using DDG Monomer to calculate ddgs for some mutants. Following the paper Kellogg-2011 I use both the Row3 (Low Resolution) and Row16 (High Resolution) protocols.

Also as is recommended in the manual page for ddg monomer (http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/d3/d...) I iterate 50 times for both protocols.

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