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protein binder interface design error

Category: 
Design

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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Pepspec - sequence sampling

Category: 
Design

Hello,

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:

-in:file:s ppk_complex_0001.pdb

-pepspec::pep_chain B
-pepspec::pep_anchor 1
-pepspec::n_append 9
-pepspec::n_peptides 10000

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Wheel Installation error

Category: 
Compilation

Hello all,
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.

Any hints?

Best,
Brandon

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genkic mover produced an unwanted HN - CA bond

Category: 
Loop Modeling

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.

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FARFAR2 - Extra Minimize Hangs on Submittal

Category: 
Nucleic Acids

Hello,

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. 

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ERROR: Assertion `static_cast< size_type >( i - l_ ) < super::size()` failed. ERROR:: Exit from: src/utility/vectorL.hh line: 42

Category: 
Structure prediction

Hi,

I'm trying to generate model from CM. There is error message shown as the topic (as uploaded crash file).

'Singal 6' is given at stage 4:

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Cannot compile Rosetta with "extras=hdf5" flag

Category: 
Compilation

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?

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Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations

Category: 
Structure prediction

Hi,

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?

Thanks,

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