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Interface Design

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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"Unhandled exception" error while running on Windows


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 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!


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Specifying disulfide bonds

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.


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high resolution protein docking doesn't work

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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question about protein docking results

I am using the docking_protocol.linux for high resolution complex. I found there are many parameters in *.fasc file such as:

fa_atr fa_dun fa_rep fa_sol hack_elec hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb interchain_contact interchain_env interchain_pair interchain_vdw.

So, I am wondering which one would be a measurement for final model selection?

BTW, could this protocol support MPI multiple CPU running?


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