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docking in rosetta 3.3

hi.................
i am new to rosetta. I have installed rosetta 3.3 in ubuntu linux 10.10. I wanted to do protein-protein docking & protein-peptide docking. so, can u help me to do this things. i have read the manuals of rosetta3.3 but i m unable to understand it correctly.Can you show me some direction to do this things & also how to create input files .pdb with only atom details for docking n other things also.............

thank you.....................

Post Situation: 

Surface accessible residue as a constraint.

Hi

I wonder if anyone has any ideas how I might do this. I have a protein where I know some of the surface exposed residues (from labelling experiments) and I was wondering if there was a way to use this as a constraint in structure production. For example is it possible to say that the amines (Nz) of lysines X,Y and Z must be solvent exposed?

Thanks for any suggestions you might have.

Best wishes

Chris

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Rosetta 3.3 Compilation error

Hello. I am quite new to Rosetta, Cygwin, Scons. I am currently running Windows 7 64-bit. I so far have installed MinGW, cygwin, python 2.7.2 and scons.

Here is the message I get from cygwin:

$ scons.bat bin mode=release
scons: Reading SConscript files ...
Traceback (most recent call last):
File "C:\users\jaewon\documents\source\rosetta\rosetta_source\SConstruct", line 139, in main
build = SConscript("tools/build/setup.py")
File "C:\Python27\Scripts\..\Lib\site-packages\scons-2.1.0\SCons\Script\SConscript.py", line 614, in __call__
return method(*args, **kw)

Post Situation: 

Symmetry Docking and Clustering with Ligands

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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