# Unsolved

The problem hasn't been solved

## 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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## Antibody scoring

Category:
Scoring
ROSIE

Hi,

I am wondering what the scores that are provided in the score file of an antibody job mean. Does a more negative score mean that a model is expected to be closer to the native structure?

Thanks!

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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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## RosettaDock-3.2 output

Category:
Docking

I do not how should select the score term. It seems that they give totally different results.

For the three parameters used in CAPRI, fnat, lRMS and iRMS, can they be calculated without the native model?

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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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