Hi! I ran into a problem when I was repeating the article "Design of protein binding proteins from target structure alone". The protocol I was followed is cao_2021_protocl_guide.txt. The step I was running is 12th: running a pilot job which is a protein interface design. could anyone help solve this problem?
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I am using Pepspec to optimize a 10mers peptide sequence to better binding to a membrane protein. In the design, I kept the first residue constant, while mutating the rest by all 20 amino acids. The flags file is the following:
I'm trying to implement the wheel-based installation for rosetta, and was getting the following error. I'm currently running the Ubuntu environment on Windows 10.
pip install pyrosetta-2020.25+release.d2d9f90b8cb-cp35-cp35m-linux_x86_64.whl
Defaulting to user installation because normal site-packages is not writeable
ERROR: pyrosetta-2020.25+release.d2d9f90b8cb-cp35-cp35m-linux_x86_64.whl is not a supported wheel on this platform.
I ran the tutorial placed in
demos/tutorials/GeneralizedKIC/exercise1/ and successfully produced 10 output structures. However, the residue ALA32 that was encompassed by the genkic mover has unwanted HN - CA bond and HN_CB bond. All the 10 output structures have this problem, and I've attached three of them. I tried to FastRelax the strucutre after genkic mover, but the unwanted bonds were still kept.
I have attempted several times to start a new FARFAR2 run that uses one or two template PDBs for homology modeling. This seems to work well with default settings, but I need to supply data in the "Residues for 'extra' minimization" text field to relax the homology model near its endpoints. When I include data in this field, it causes the popup "Submitting FARFAR2 job..." to display indefinitely. I waited overnight to see if this was just slowing things down quite a bit, but no success.
Hello. I'm having trouble compiling Rosetta on an AWS Ubuntu 22.04 instance, using scons with the extras=hdf5 flag. The problem seems to be with finding the HDF5 libraries.
My question - how can I successfully compile Rosetta with the extras=hdf5 flag?
I installed rosetta_bin_linux_2021.07.61567 mode=debug and then ran Rosetta CM Hybridization. However, it gives the error messages as 'Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations'. I have deleted everthing with 'rosetta_bin_linux_2020.08.61146_bundle'. I do see this rosetta_citations file in my current 'rosetta_bin_linux_2021.07.61567_bundle/database/citation path. May I know why it looks for the citations file in my earlier old version? How to fix it?