The problem hasn't been solved
Hi,
Binding score is calculated as the total score of complex minus the sum of the scores of unbound two partners, should I repack the side-chain of two partners after seperate the complex, or just score them without repacking?
Since Rosetta 3.2 is not yet aivailable. Is there any plan to provide development snapshot or read access to svn?
Knut J
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.
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!
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.
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
Hi!
I would like to know if Rosetta DDG can be used to calculate the entropy as well the enthalpy of various mutations.
Thank you in advance,
Abdullah
Hi!
I am new to linux and gcc and scons. I am trying to install Rosetta 3.1 on ubuntu 10.10. The installation seems to be working properly until it gives this error:
I am working on the Pyrosetta tutorial and I am trying to use protein fragments. Howevere there is a problem since the Robetta server keep on failing.
I am submitting this fasta file.
>poly_
AAAAAAAAAAAAAAAAAA
Is there anything wrong with my fasta format-
Knut J
how to do cluster after low resolution protein-protein docking? I follow the manually and use docking.sc file as cluster input file for clustering, but it doesn't work.
THX